qbasepileup compound snp mode

java -jar qbasepileup.jar -m compoundsnp ...

In this mode, qbasepileup reads one or more BAM files, a reference genome, and a file containing positions of compound SNPs (SNPs that sit next to each other). It finds the reference genome base at the compound SNP positions as well as the bases found at that position in all reads aligned to that region. Coverage per nucleotide is reported and the total coverage at that position is reported. By default, the filter is: and( Flag_DuplicateRead==false, CIGAR_M>34, MD_mismatch<=3, option_SM>10 )

Options

This mode is for compound SNPs, i.e. SNPs that are next to each other. It is very similar to snp mode except:

• Only dcc1 format (-f) is currently accepted
• Default filter is: and(Flag_DuplicateRead==false, CIGAR_M>34, MD_mismatch<=3, option_SM>10)