Dear all,
I have trouble to understand how bedtools computing coverage. I have vcf file (generated from Illumina somatic caller) - I was created bed file from my vcf.
Then I try to compute coverag with bedtools and I have for the same coordinate different coverage. Could you help me to explain why? Probably some reads where filter out during vcf calling algorithm.
Output is:
coverage in vcf:
chr13 32890572 DP=45048
chr13 32893197 DP=1494
chr13 32899359 DP=12809
chr13 32900176 DP=57850
chr13 32900177 DP=61728
and in my bedtools output:
chr13 32890572 32890573 47857 1 1 1.0000000
chr13 32893197 32893198 1686 1 1 1.0000000
chr13 32899359 32899360 15673 1 1 1.0000000
chr13 32900176 32900177 65461 1 1 1.0000000
chr13 32900177 32900178 65461 1 1 1.0000000
Note, that my vcf coverage is before filtering.
Can anybody now why is this different? And if you can explain (mathematically) how bedtools computing coverage? Is it sum of all coverage in the interval and then divide length of interval? Of it is just sum of all coverage in interval?
Thank you so much for clarification.
Paul.
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