Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samtools bcftools no FQ value

    Hello,

    I'm using the samtools/bcftools/vcfutils pipeline to call consensus sequences. However, I always get an warning:

    Use of uninitialized value $q in numeric lt (<) at vcfutils.pl line 508, <> line 16742.
    Use of uninitialized value $q in addition (+) at vcfutils.pl line 518, <> line 16742.

    Which seams to be a problem with the FQ values. I checked the bcftools view -cg output and it doesn't record the FQ value. So, I think that's what's causing the problem.

    Any idea why it doesn't provide the FQ value? And how to make it to? (I tried samtools 0.1.18 and 0.1.19).

    Thanks,
    Stefan

  • #2
    For starters, it would help if you posted your command lines, the versions of each piece of software, and a sample line from your .vcf

    I'm wondering if you are using a very old version of samtools

    Comment


    • #3
      Hi,

      I use:

      samtools mpileup -uf "$REFSEQ" ${bn}.sorted.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq > ${bn}.fq

      So the standard consensus call.

      The output is here:

      ##fileformat=VCFv4.0
      ##samtoolsVersion=0.1.18 (r982:295)
      ##fileformat=VCFv4.0
      #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT processed_MS83_S20_L001.dup.sorted.bam
      NC_002008 1 . G T 46 . DP=11;VDB=0.0000;AF1=0.500;AFE=0.500;DP4=3,0,8,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 76,0,85:0/1:78
      NC_002008 2 . T . 99 . DP=89;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=81,0,8,0;MQ=37;PV4=1,1,0.0005,1 P0
      NC_002008 3 . T . 99 . DP=154;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=101,0,0,0;MQ=36 PL 0
      NC_002008 4 . A . 99 . DP=260;AF1=0.000;AFE=0.000;DP4=133,73,0,0;MQ=38 PL 0
      NC_002008 5 . A . 99 . DP=262;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=134,73,0,0;MQ=38 PL 0
      NC_002008 6 . T . 99 . DP=263;VDB=0.0000;AF1=0.000;AFE=0.000;DP4=133,73,0,0;MQ=39 PL 0

      I'm using the newest and the previous version of samtools. 0.1.18 and 0.1.19 like I wrote in my post. Bcftools and vcfutils come with samtools. So they all are up to date.

      Thanks,
      Stefan

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:23 AM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-17-2024, 06:54 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-14-2024, 07:24 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-13-2024, 08:58 AM
      0 responses
      18 views
      0 likes
      Last Post seqadmin  
      Working...
      X