Hi, I want to run fpfilter (VarScan false-positive filter) to remove false positives from the vcf files; however I stuck in the step of generating readcount from my vcf file. This is my command:
bam-readcount -f hg38.fa -q 1 -b 20 -l all.Somatic.hc.var tumor.sorted.bam > all.Somatic.hc.readcount
I get this error:
Minimum mapping quality is set to 1 [bam_index_load] fail to load BAM index. BAM indexing file is not available.
Can anyone help me out? Thanks!