qBasePileup Compound SNP

• Options

In this mode, qbasepileup is 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 componud 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 ie SNPs that are next to each other.
as per qbasePileup SNP mode except:

• Only dcc1 format is currently accepted
• Default filter is: "and(Flag_DuplicateRead==false , CIGAR_M>34 , MD_mismatch <= 3 , option_SM > 10)"
• For mode option use:

-m compoundsnp