I am trying to run bam-readcounts and fpfilter.pl on my VarScan2 output but most of my variants "failed to get readcounts for variant allele".
My output is not vcf and I did not find anything related to lower and upper cases (as was mentioned in another forum).
Any idea what might be the problem?
bam-readcounts comman line:
bam-readcount -q 1 -b 20 -f /media/Data/Anat_Data/Ref_genome/human_g1k_v37.fasta no_R2_mapped_sorted.bam -l /media/localData/Anat/HCC_mut/DesignDocument/full_Regions_new output.basename.copy.snp.Somatic > varScan.variants.copy.snp.Somatic.readcounts
fpfilter command line:
perl /usr/local/bin/fpfilter.pl output.basename.copy.snp.Somatic.hc.filter varScan.variants.copy.snp.Somatic.readcounts --output-basename varScan.copy.snp.Somatic.hc.filter
17 failed to get readcounts for variant allele
0 had read position < 0.1
0 had strandedness < 0.01
1 had var_count < 4
0 had var_freq < 0.05
0 had mismatch qualsum difference > 50
0 had mapping quality difference > 30
0 had read length difference > 25
0 had var_distance_to_3' < 0.2
0 passed the strand filter