Calculating coverage of SNPs

[aprilw]

Hello all,

I'm having a problem calculating the depth of coverage of a set of known variants (SNPs). What I want to know is 1) what percentage of known variant sites are captured in my sequencing, 2) to what depth are those variant sites sequenced to (ie. average depth, >5 reads, >10 reads, ect).

The problem is I have hundreds of large bam files from separate experiments, and a very large set of SNPs, so I can't spare the space to output a samtools depth file and just iterate through. I was wondering if there is a tool that alone or in combination with basic unix commands will give me what I want. I have tried using coverageBed (bedtools v. 2.17.0), but I can't seem to get it to give me what I want.

I have the SNPs in a vcf file (that bedtools errors out on), and a bed file that looks like this:

M 647 648 A/C +
M 934 935 G/A +
M 941 942 T/C +
M 1098 1099 T/C +
M 1222 1223 G/A +
M 1247 1248 T/C +
M 1520 1521 G/A +
M 1692 1693 C/T +
M 1831 1832 A/G +
M 1855 1856 G/A +

But bedtools doesn't find any coverage or overlap of these SNPs (which is not true).

Thanks in advance.
April