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