Jonathon Tessmann

I've grep'd the lines from the mpileup file that matched the coordinates in my vcf-validator output: 1 9440393 G 8 .,...-3GAA.-3GAA.. O<MCCE:D 8 .-6GAAGAA,-6gaagaa..-6GAAGAA,... EBDH0?CB 1 93128514 T 14 ,,,,.,-1a,,,-1a,,,+1a,-1a, >>:>^=<>>>?9A: 11 ,,,,,+1a,+1a,,+1a,,, =ABB?=9>=:3 1 118501390 C 14 ...+1T.+1T....+1T.+1T..+1T.+2TT.. GHDDDDDDCCDDEE 13 ....+1T.-1T...+1T.-1T.-1T... HHBEEEDCDEEEA

I am trying to run Varscan v2.3.9 and samtools v1.3.1 using the following commands to generate pileup files and to perform somatic variant calling: samtools mpileup -f reference.fasta -q 1 -B normal.bam tumor.bam > normal-tumor.mpileup java -jar VarScan.jar somatic normal-tumor.mpileup normal-tumor.output.vcf --mpileup 1 --output-vcf 1 These commands run fine, however the snp and indel vcf's I recieve as output are malformed. I checked their format using vcf-tool's vcf-validator, and got this message:...