No common samples in VCF and BAM headers, so nothing could possibly be phased!

alisonewralisonewr Member
edited November 2015 in Ask the GATK team

I want to phase some DNA-seq data.

java -jar GenomeAnalysisTK.jar -T ReadBackedPhasing -R ref.fasta -I readnames.bam --variant test.vcf -L Chr.list -o phased_SNPs.vcf --phaseQualityThresh 20.0

My vcf file looks like this and only contains information for 1 sample

fileformat=VCFv4.0

source=pileup_to_vcf.pyV1.2

INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

INFO=<ID=SAF,Number=.,Type=Float,Description="Specific Allele Frequency">

FILTER=<ID=DP,Description="Minimum depth of 10">

FILTER=<ID=SAF,Description="Allele frequency of at least 0.3 with base quality minimum 0">

CHROM POS ID REF ALT QUAL FILTER INFO

NC_024331.1 131 . G GA . PASS SAF=0.655738;DP=61
NC_024331.1 147 . C G . PASS SAF=0.320000;DP=25
NC_024331.1 422 . C A . PASS SAF=0.414545;DP=275

I previously had an error message saying my bam file did not have read names. I ran
java -jar AddOrReplaceReadGroups.jar I=sorted.bam O=readnames.bam RGLB=LaneX RGPU=NONE RGSM=AnySampleName RGPL=illumina

Now I am getting an error

ERROR
ERROR MESSAGE: No common samples in VCF and BAM headers, so nothing could possibly be phased!

Is there somewhere in the header of the vcf I can add AnySampleName?

Thanks!!

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    The problem is deeper than that -- you need to have genotype calls for your samples in the VCF. Otherwise there's nothing to phase. Have you read the documentation about phasing?

  • alisonewralisonewr Member
    edited November 2015

    Thanks! So as I only have one sample, does that mean I have to specify
    -v, --VCF Compute genotype likelihoods and output them in the variant call format (VCF) when I run samtools mpileup?

    And as my bam file is only one sample, it has no sample information in the header. How do I fix this?

    Thanks very much!!

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