Question

[awata-hiroko]

Hi,

I tried to estimate PCR duplicates ratio of my samples using it. I did "extract_duplicates" command using vcf file made by "samtools mpileup" using my samples.
The output files from "exact_duplicates" command are strange for me because the contents from multiple samples are almost same and "PCR duplicates marked 0 total-reads 0 frac -nan discarded 49244807" and "#clusters
total reads (PE=1) 0 unique-reads 0 duplicates:0, duplication rate -nan" were written.
My samples seems to contain many PCR duplicates (aprrox. 90% of the total) by judge of "samtools rmdup". So I don't believe the output file from "exact duplicates" (it said no PCR duplicate in my samples, right?)

So, what should I do to resolve this issue? Should I use vcf files from public databse like ENSEMBL?

[vibansal]

It seems that the input is not correct or unexpected. The program requires a VCF file with variants that should be from the same individual/sample. What type of sequence data are processing and what is the source of the vcf file?