Less SNVs with larger interval file - MuTect
Hi,
I've used MuTect to call variants on .bam files (standard procedure for exome seq, tumor vs normal) using two different interval files (both from Illumina website): Nextera Exome Capture and Nextera Exome Capture Expanded. These intervals correspond to different kit versions, with expanded kit spanning about twice more targeted regions (~60Mb vs ~30Mb). The libraries has been created using Expanded kit.
To my surprise, providing with 30Mb interval file resulted in 674 SNVs; same bam/MuTect parameters with 60Mb interval file gave 545 SNVs (here I refer to KEEP SNVs; total SNVs are also decreased when larger interval file is used).
I am going to study how these sets overlap, but anyway I cannot understand this. Even if no more additional mutations is present in regions from larger interval file as compared to smaller one, still reduction to over 100 SNV (129) seems too large. I just cant trust my data analysis when I see such things.
Did anybody experienced similar before?
Thanks,
Artem
I've used MuTect to call variants on .bam files (standard procedure for exome seq, tumor vs normal) using two different interval files (both from Illumina website): Nextera Exome Capture and Nextera Exome Capture Expanded. These intervals correspond to different kit versions, with expanded kit spanning about twice more targeted regions (~60Mb vs ~30Mb). The libraries has been created using Expanded kit.
To my surprise, providing with 30Mb interval file resulted in 674 SNVs; same bam/MuTect parameters with 60Mb interval file gave 545 SNVs (here I refer to KEEP SNVs; total SNVs are also decreased when larger interval file is used).
I am going to study how these sets overlap, but anyway I cannot understand this. Even if no more additional mutations is present in regions from larger interval file as compared to smaller one, still reduction to over 100 SNV (129) seems too large. I just cant trust my data analysis when I see such things.
Did anybody experienced similar before?
Thanks,
Artem
