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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. -
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
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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.
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bbmap callvariants.sh multisample vcf format, wrong number of fields
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:
The VCF:Code:vcf-validator tmp.vcf Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]
BBMap command:Code:#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT
I think BBMap could be a very powerful set of tools and I am expecting I am missing something pretty basic!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
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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