Hello,
I've used the following command to filter my BAM file, run samtools pileup and varscan:
samtools view -b -q 10 myBam.bam | samtools mpileup -f myRef.fasta -
| java –jar VarScan.v2.3.6.jar pileup2snp --min-coverage 6 --min-avg-qual 4 --min-var-freq 0.01 --p-value 0.05
The program ran for a while and then I got this error:
Error: Invalid format for pileup at line 820808910
chr18 74082743
It seems like a lot of people have had this issue before but I don't know how to fix it. Any help will be greatly appreciated. Thanks!!
I've used the following command to filter my BAM file, run samtools pileup and varscan:
samtools view -b -q 10 myBam.bam | samtools mpileup -f myRef.fasta -
| java –jar VarScan.v2.3.6.jar pileup2snp --min-coverage 6 --min-avg-qual 4 --min-var-freq 0.01 --p-value 0.05
The program ran for a while and then I got this error:
Error: Invalid format for pileup at line 820808910
chr18 74082743
It seems like a lot of people have had this issue before but I don't know how to fix it. Any help will be greatly appreciated. Thanks!!
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