Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • illuminaGA
    Member
    • Dec 2012
    • 71
    #1

    SNP call by samtools, but ALT is "X" QUAL is "0"

    Dear All

    I had an issue when I did SNP calling by samtools 1.1 with the following commend " samtools mpileup -f hg18chr.fa -u -v 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam -o output.vcf "

    The out put file is vcf format but all the ALTs are <X> and all the QUALs are "0"

    How can I trouble shoot? Any help is much appreciated

    Here is a sample.

    ##fileformat=VCFv4.2
    ##FILTER=<ID=PASS,Description="All filters passed">
    ##samtoolsVersion=1.1+htslib-1.1
    ##samtoolsCommand=samtools mpileup -f hg18chr.fa.fa -u -v -o mutibamtest.vcf 9098.bam 9101.bam 9103.bam 9105.bam 9107.bam 9100.bam 9102.bam 9104.bam 9106.bam
    ##reference=file://hg18chr.fa.fa
    ##contig=<ID=chr22,length=49691432>
    ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
    ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
    ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
    ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
    ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
    ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
    ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
    ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
    ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
    ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
    ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
    ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
    ##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
    ##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
    ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 9098.bam 9101.bam 9103.bam 9105.bam 9107.bam 9100.bam 9102.bam 9104.bam 9106.bam
    chr22 14436326 . T G,<X> 0 . DP=1;I16=0,0,1,0,0,0,29,841,0,0,3,9,0,0,0,0;QS=0,1,0;SGB=-0.0293345;MQ0F=0 PL 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 0,0,0,0,0,0 4,3,0,4,3,4 0,0,0,0,0,0
    chr22 14436327 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436328 . G <X> 0 . DP=1;I16=1,0,0,0,26,676,0,0,3,9,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436329 . G <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,3,9,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436330 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,4,16,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436331 . C <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,5,25,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436332 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,6,36,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436333 . G <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,7,49,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436334 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,8,64,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436335 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,9,81,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436336 . C <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,10,100,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436337 . C <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,11,121,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436338 . A <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,12,144,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436339 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,13,169,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436340 . A <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,14,196,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436341 . G <X> 0 . DP=1;I16=1,0,0,0,29,841,0,0,3,9,0,0,15,225,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436342 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,16,256,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436343 . A <X> 0 . DP=1;I16=1,0,0,0,27,729,0,0,3,9,0,0,17,289,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436344 . A <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,17,289,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    chr22 14436345 . G <X> 0 . DP=1;I16=1,0,0,0,28,784,0,0,3,9,0,0,16,256,0,0;QS=1,0;MQ0F=0 PL 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 0,3,4 0,0,0
    Tags: None
    • dpryan
      Devon Ryan
      • Jul 2011
      • 3478
      #2
      The command you're looking for is "bcftools call ...", just give it that file.

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by SEQadmin2




          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
          Yesterday, 06:46 AM
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating          ...
          10-14-2026, 09:55 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        29 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:57 AM  
        Single-Cell Sequencing of 5 Million Immune Cells Links Genetic Variants to Disease by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:51 AM
        0 responses
        19 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:51 AM  
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        71 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        48 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        View All
        Working...