Hi Everyone,
So I have human exome data with mean coverage of about 150 X and I wish to apply filtering on VCF file that I obtained with SAMtools + BCFtools. I am confused regarding what should be max Read Depth (DP) parameter (-D) for varFilter. As in SAMtools source page it is recommended that max DP should 2x of mean coverage.
http://samtools.sourceforge.net/samtools.shtml
As far as I understand DP is the average number of read that passed SAMtools filtering (while calling variant), please correct me if I am wrong. So my question is shouldn't be the high DP meaning suggest high confidence of the variant (SNP/Indel) for the position than why set max limit for DP ?
Thanks in advance,
So I have human exome data with mean coverage of about 150 X and I wish to apply filtering on VCF file that I obtained with SAMtools + BCFtools. I am confused regarding what should be max Read Depth (DP) parameter (-D) for varFilter. As in SAMtools source page it is recommended that max DP should 2x of mean coverage.
http://samtools.sourceforge.net/samtools.shtml
As far as I understand DP is the average number of read that passed SAMtools filtering (while calling variant), please correct me if I am wrong. So my question is shouldn't be the high DP meaning suggest high confidence of the variant (SNP/Indel) for the position than why set max limit for DP ?
Thanks in advance,