Dear all,
I used Bowtie and BWA to align my paired-end reads from Illumina Genome Analyzer to the reference genome. I then used Varscan to call variants. However, the SNVs I get, aren't exactly the same.
Does anybody know a way to compare both files with SNVs so that I will get a file with SNVs present in both files and then separate files containing the resultant SNVs?
Thanks a lot!
Lien
I used Bowtie and BWA to align my paired-end reads from Illumina Genome Analyzer to the reference genome. I then used Varscan to call variants. However, the SNVs I get, aren't exactly the same.
Does anybody know a way to compare both files with SNVs so that I will get a file with SNVs present in both files and then separate files containing the resultant SNVs?
Thanks a lot!
Lien
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