bbmap callvariants.sh multisample vcf format, wrong number of fields

Greg · 04-04-2018, 09:46 AM

Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:

Code:

vcf-validator tmp.vcf 
Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]

The VCF:

Code:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT

BBMap command:

Code:

callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa 
#ive also tried using the output command, no change
callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa vcf0=S1,S2,S3,S4,S5,S5
#As well as each sample using the "in" command
callvariants.sh multisample=t in=S1.sam,S2.sam,S3.sam,S4.sam,S5.sam,S6.sam out=tmp.vcf ref=genome.fa overwrite=t vcf0=AO,GG,OG,SF,TH,Tum

I think BBMap could be a very powerful set of tools and I am expecting I am missing something pretty basic!

Brian Bushnell · 04-04-2018, 10:10 AM

Hi Greg,

Sorry about that, there was a bug that slipped in around v37.87 with regards to multisample VCF names. It's fixed in v37.96 which I will release this week.

-Brian

Greg · 04-04-2018, 10:27 AM

Okay cool, thanks for the quick response!

denisDDS · 04-24-2018, 05:45 AM

Same error here: downloaded BBMap 2 weeks ago, finishing my snp calling pipeline today, same problem and discovering the patch went out 10 days ago...

Thx for the fix

Brian Bushnell · 04-24-2018, 09:42 AM

Oh, yep - it's fixed now, sorry for not mentioning that!

denisDDS · 04-25-2018, 01:00 AM

I have another problem: when using vcf0=, followed by files locations separated by comma, callvariants.sh create subdirectory instead of just creating files at specified location.

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04-04-2018, 10:10 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	Hi Greg, Sorry about that, there was a bug that slipped in around v37.87 with regards to multisample VCF names. It's fixed in v37.96 which I will release this week. -Brian

04-04-2018, 10:27 AM	#3
Greg Member Location: British Columbia Join Date: Oct 2009 Posts: 31	Okay cool, thanks for the quick response!

04-24-2018, 05:45 AM	#4
denisDDS Junior Member Location: France Join Date: Feb 2013 Posts: 6	Same error here: downloaded BBMap 2 weeks ago, finishing my snp calling pipeline today, same problem and discovering the patch went out 10 days ago... Thx for the fix

04-24-2018, 09:42 AM	#5
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	Oh, yep - it's fixed now, sorry for not mentioning that!

04-25-2018, 01:00 AM	#6
denisDDS Junior Member Location: France Join Date: Feb 2013 Posts: 6	I have another problem: when using vcf0=, followed by files locations separated by comma, callvariants.sh create subdirectory instead of just creating files at specified location.