Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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:

    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!

  • #2
    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

    Comment


    • #3
      Okay cool, thanks for the quick response!

      Comment


      • #4
        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

        Comment


        • #5
          Oh, yep - it's fixed now, sorry for not mentioning that!

          Comment


          • #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.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X