Hello all, I am trying to call somatic variants using VarScan.v2.4.3 from merged bam files. Here is the sript used to run the same.
java -Xmx64g -jar VarScan.v2.4.3.jar somatic <(samtools mpileup -l AmpliSeqExome.hg38.bed --no-BAQ -f "$bwa_ref".fa Normal_merged.sorted.bam Tumor_merged.sorted.bam) varscan_vcf/variant --mpileup 1 --output-vcf
The run is executed without any errors and the out put is pasted below.
Min coverage: 8x for Normal, 6x for Tumor Min reads2: 2 Min strands2: 1 Min var freq: 0.2 Min freq for hom: 0.75 Normal purity: 1.0 Tumor purity: 1.0 Min avg qual: 15 P-value thresh: 0.99 Somatic p-value: 0.05 Reading input from /dev/fd/63 Reading mpileup input... 23064925 positions in mpileup file 22855806 had sufficient coverage for comparison 22796450 were called Reference 0 were mixed SNP-indel calls and filtered 0 were removed by the strand filter 54812 were called Germline 560 were called LOH 3979 were called Somatic 5 were called Unknown 0 were called Variant
The generated vcf however has only variants till chr7 and no more. The total line counts in vcf files for both the generated snp and indel vcf files is not more than 36000 (~18k + ~18k) and the file size is just around 3 MB.
I have run the same on multiple files and every single run has produced similar output.
I have also checked the presence of other chromosomes in our bam file. Can anyone point to a reason there are no calls after chr7?