https://github.com/brentp/vcfanno - fix for QUAL of 256

QUAL of 256 was previously set to ".". Thanks to @ToonRosseel for the fix.

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Published by brentp 11 months ago

https://github.com/brentp/vcfanno - v0.3.6

fix bug for SVs with END= as final field

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Published by brentp about 1 year ago

https://github.com/brentp/vcfanno - fix regression from 0.3.4

This fixes a major bug in v0.3.4 (#150). Please update.

Full Changelog: https://github.com/brentp/vcfanno/compare/v0.3.4...v0.3.5

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Published by brentp over 3 years ago

https://github.com/brentp/vcfanno - v0.3.4

This release fixes and issue where the FORMAT column was added to the VCF header when no samples were present.

Full Changelog: https://github.com/brentp/vcfanno/compare/v0.3.3...v0.3.4

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Published by brentp almost 4 years ago

https://github.com/brentp/vcfanno -

This contains minor usability fixes.

• 0314e53 - add vcfanno version to header (#140)
• c4c0ae9 - update travis
• 49ef500 - non-zero exit when no args are given
• 6e5a12a - fix help which still mentioned js.
• 9f857a9 - handle missing value in postannotation. closes #116
• 1d140d4 - Misleading Flatten error message (#119)
• 8ffa89c - fix example table format of markdown (#115)

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Published by brentp over 4 years ago

https://github.com/brentp/vcfanno - general fixes and by_alt

this release has minor fixes to by_alt and other bugs:

• 8c692e2 - handle by_alt + float correctly (#113) (12 days ago)
• deeeee3 - Fix always falling back to non-bgzip reader (#109) (8 weeks ago)
• 54bcc00 - add go 1.11 (5 months ago)
• cc8048d - add release target to makefile (5 months ago)
• 5683246 - Add Makefile (#103) (5 months ago)
• 16701a1 - closes #99 (6 months ago)

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Published by brentp almost 7 years ago

https://github.com/brentp/vcfanno - fix for empty description

v0.3.1

• allow empty description in VCF header (sigven/pcgr#49)

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Published by brentp over 7 years ago

https://github.com/brentp/vcfanno - minor updates

v0.3.0

• support for NON_REF to match any ALT allele (#92)
• more work on multiple alts (#87)

there should be ~3-5% speed improvement thanks to improvements in the go compiler.

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Published by brentp almost 8 years ago

https://github.com/brentp/vcfanno - csi support

this release adds support for CSI. this can greatly speed up dense files like CADD and even gnomAD or ExAC.

to use, simply index your file with tabix as, e.g.:

tabix -m 12 --csi $file

and vcfanno will prefer the .csi index over the .tbi.

refer to the performance page for how to optimize. in brief, setting export IRELATE_MAX_GAP=1000 seems to give good results. Please experiment and let me know what works for you. I can get ~60% speed improvement using csi'd ExAC to annotate clinvar with the above changes.

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Published by brentp over 8 years ago

https://github.com/brentp/vcfanno - bug fix

v0.2.8

• fix fo #71 for out of bounds warning followed by panic.

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - improvements for multiple alts (self, by_alt ops)

v0.2.7

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• new op setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements equal to the number of alternates. If there are > 1 annos for a given site, later values will overwrite previous.
• new op by_alt that will have Number=A and will append multiple annotations for the same alternate (from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333 when the 1st alternate has a single value and the 2nd alternate has 2 values.

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - by_alt and other multi-allelic fixes

v0.2.7 (dev)

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• new op setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements equal to the number of alternates. If there are > 1 annos for a given site, later values will overwrite previous.
• new op by_alt that will have Number=A and will append multiple annotations for the same alternate (from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333 when the 1st alternate has a single value and the 2nd alternate has 2 values.

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - multiple alts, multiple lines, overwrite.

v0.2.7 (dev)

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• add setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements equal to the number of alternates. If there are > 1 annos for a given site, later values will overwrite previous.

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - fixes for Number=A, op=self

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• add setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - fix race

v0.2.6

• fix race condition from 0.2.4 by reverting some speed improvements from that release.

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Published by brentp about 9 years ago

https://github.com/brentp/vcfanno - div2

v0.2.4

• 30-40% speed improvement when annotating with few, large files by parallelizing decompression.
• handle multiple values to div2 (mostly for multi-allelics)
• if _af or af_ is in the name then make Number=A for a postannotation.

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - FILTER and delete

v0.2.3

• allow pulling the 'FILTER' field from a VCF by specifing 'FILTER' in the fields
• add new op for postannotation only 'delete' which can be used to remove fields from the INFO.
• use Description from annotation as Description in annotated file (thanks @xuyangy for the implementation #43)

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - postannotation + ID fix

v0.2.2

• wholely fix order of error checking from postannotation (affects users using ID annotation) (thanks @vladsaveliev)

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - postannotation ID fix

v0.2.1

• correct order of error-checking on return from postannotation (affects users using ID annotation)

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - multiallelics!

This support brings full and proper support for multiallelics. Any annotation file and field that has Number=A in the header can be used to correctly annotate a query file with ops=['self']. See: http://brentp.github.io/vcfanno/#multi-allelics for more details.

v0.2.0

• proper support for multi-allelics in query and in annotation with op="self"
• allow post-annotation to set ID column

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno -

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - fix END in non VCF files with ref and alt columns

v0.1.1

• set number=1 when op=min see #40
• fix when we get -0 converted to just '-' (#42)
• when an annotation bed file has a header with 'ref' or 'reference' and 'alt' or 'alternate', then match on the ref and alt values defined in those columns (not just on position as for bed).
• (vcfgo) allow double-digit number in header thanks @chapmanb
• correct END position when using ref and alt from a file with only a position (infer end as start + len(ref)) [thanks Tomas].
• about 15% performance improvement mostly due to go1.8

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - v0.1.1 RC1

v0.1.1

• set number=1 when op=min see #40
• fix when we get -0 converted to just '-' (#42)
• when an annotation bed file has a header with 'ref' or 'reference' and 'alt' or 'alternate', then match on the ref and alt values defined in those columns (not just on position as for bed).
• (vcfgo) allow double-digit number in header thanks @chapmanb

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Published by brentp over 9 years ago

https://github.com/brentp/vcfanno - v0.1.0

v0.1.0

This release contains usability improvements and some additional functionality. Tar/zips below contain readme and examples. Just the binaries for linux-64 and osx 64 are also provided for ease of wgetting. - drastically reduce the warning message output. - add field=['DP2'] for bam files which reports number of forward and reverse reads overlapping a variant. value returned can be replicated with: samtools mpileup -A -x -Q 1 -q 1 -r chrom:pos-pos $bam - add op=sum - expose ref and alt to lua. (thanks @roryk)

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Published by brentp almost 10 years ago

https://github.com/brentp/vcfanno - v0.0.11

Version 0.0.11 contains a number of usability improvements along with fixes for the -ends stuff for annotating SVs. It should also have about 20% speed improvement thanks to the improvements in the go runtime itself.

v0.0.11

• when op=self, pull Number from the annotation file (previously Number was always 1)
• when op=concat or op=uniq user Number=.
• when name ends with 'float' 'int' or 'flag' that is used to determine the Type in the output and that is then stripped from the name. So, e.g. with ` names=["afespaafloat"] ` The resulting header will be:

```

INFO=<ID=afespaa,Number=1,Type=Float,Description=...

`` - fix regression with CIPOS/CIEND when using-endswith structural variants. (Thanks to Liron for reporting) - fix bug with uniq not uniq-ing (Thanks Liron for reporting) - improve error messages from lua (Thanks Komal Rathi for the test-case provoking this change). - improve handling of multiple values (usually due to multiple alts) formaxandmin. Now, if we have, e.g. var1:SAS=0.22,0.33 and var2:SAS=0.25 thenmax` will give 0.33. This change makes max and min recursive so they'll call themselves on nested slices. Thanks @snashraf for reporting.

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Published by brentp about 10 years ago

https://github.com/brentp/vcfanno - 0.0.10

In addition to performance and usability improvements, this release fixes some regressions. A functional test-suite has been expanded to improve these.

v0.0.10

• allow using postannotation even if not all requested fields were found for a given variant.
• restore ability to have bams as annotation files. Can pull mapq and coverage. See examples/conf.toml
• fix regression where output was not in sorted order.
• fix regression that resulted in "too many open files" error.
• expand test-suite.
• fix bug found when using max() op

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Published by brentp over 10 years ago

https://github.com/brentp/vcfanno -

See below for full list of improvements. The biggest bug-fix is to fix a memory leak seen when annotating large files. The biggest change is to convert the scripting engine from javascript to lua. The reason for this was to improve the speed of user-defined functions. Now, functions defined in lua should be nearly as fast as the built-in functions but provide endless customization

v0.0.9

• restore ability to take query file from STDIN (no tabix required).
• fix memory leak. memory use now scales with number of procs (-p).
• added new op 'self' which should be used for most cases when matching on ref and alt as it determines the type from the annotation header and uses that to update the annotated header with the correct type.
• new documentation site
• [[postannotation]] allows modifying stuff in the query VCF after annotation (or instead). See examples on the documentation site.
• convert scripting engine to lua from javascript
• add CADD conversion script and example

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Published by brentp over 10 years ago

https://github.com/brentp/vcfanno - parallel chromsweep.

This is a major change to vcfanno that allows use of parallel chromsweep. This removes several problems (namely chromosome ordering) with chrom-sweep. See this design document for more details.

The list of changes are:

v0.0.8

• parallel chrom-sweep (removes problems with chromosome sort order).
  • as a result, files are required to be tabix'ed.
  • the chromosome sort order is no longer important.
  • new -p flag indicates number of processes to use.
• fix bug in SV support of CIPOS, CIENDS
• huge speed improvement (can annotate ~30K variants/second with 10 cpus).
• remove server and cadd support (will return soon).
• fix bug where header is not updated.
• respect strict when -ends is used.

Thanks to @sigven for reporting several issues that arose as a result of the major code-changes.

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Published by brentp almost 11 years ago

https://github.com/brentp/vcfanno - server, speed, SVs

v0.0.7

• better support for flags. e.g. can specify a flag from js by ending the function name with _flag
• [irelate] error if intervals are out of order within a file.
• -base-path argument replaces basepath in .toml file
• [vcfgo] report all headers in original file.
• integrated server to host annotations
• -ends argument will now use CIPOS and CIEND to annotate the left and right interval of an SV. If CIPOS and CIEND are undefined for a given interval, the ends will not be annotated.
• for MNPs, cadd score is reported as a list of max values (of the 3 possible changes) for each reference base covered by the event.
• fix bug in CADD annotation and provide CADD v1.3 download
• ~25-30% speed improvement. from a modest laptop: *annotated 10195872 variants in 28.97 minutes (351984.0 / min

If you just want a linux binary without support files, it is here

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Published by brentp almost 11 years ago

https://github.com/brentp/vcfanno - CADD!

CADD is supported. Download encoded (11GB file) from:

https://s3.amazonaws.com/vcfanno/caddv1.2.bin https://s3.amazonaws.com/vcfanno/caddv1.2.idx

and update path in conf

v0.0.6

• support for CADD
• concat defaults to | separator
• speed improvements (vcfgo info field)
• natural sort is default. use -lexographical to

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Published by brentp about 11 years ago

https://github.com/brentp/vcfanno - v0.0.5

v0.0.5

• allow natural sort (1, 2, ... 9, 10, 11 instead of 1, 10, 11 ..., 19, 2, 20) via flag
• vcfgo: handle lines longer than 65KB major
• vcfgo: fix error reporting
• irelate: report warning when chroms out of order

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Published by brentp about 11 years ago

https://github.com/brentp/vcfanno - v0.0.4

v0.0.4

• performance improvements for Javascript ops with pre-compilation.
• bam: annotate with mapq and seq for mapping-quality and sequence respectively.
• api now returns a channel on which to recieve annotated Relatables
• vcfgo: fix printing of INFO fields with multiple values (thanks to Liron for reporting).
• vcfgo: fix writing of ##SAMPLE and ##PEDIGREE headers. (thanks to Liron)

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Published by brentp about 11 years ago

https://github.com/brentp/vcfanno - bed, custom js, API

v0.0.3

• custom ops with javascript. see example conf and custom javascript
• proper support for variants.
• option to annotate BED files. (this is automatic, just use a bed file as the query).
• vcfanno has an api so it can be use from other progs.

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Published by brentp about 11 years ago

https://github.com/brentp/vcfanno - support for annotating the ends of variants (for CNVs and SVs)

This release adds much more test-coverage (>80%).

It also provides a feature for annotating large variants where we want to know about, e.g. the breakpoints of structural variants. If the -ends flag is specified from the command-line, then in addition to the annotation of the entire interval (as in the default mode), each variant will be annotated by what overlaps its 1-base left end (prefixed by "left") and its 1-base right end (prefixed by "right"). The left and right annotations are only done for intervals longer than 1-base.

It also adds the -permissive-overlap flag which tells vcfanno that any overlap is sufficient to add an annotation. In default mode, it requires that they also share the REF and at least 1 ALT allele. (this is used implicitly for the above -ends parameters).

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Published by brentp about 11 years ago

https://github.com/brentp/vcfanno - initial release

initial release of vcfanno. binaries for linux, windows, mac 32/64 bit provided.

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Published by brentp about 11 years ago