Dear all,
I was wondering if there is a standard "coverage" for exomic SNP calling in tumor_vs_healthy samples (same patient). As we know, tumor samples have an intrinsically higher mutability (Parsons et al., 1993). I was thinking of applying a threshold of at least 20X for the healthy one, and 50X for the tumor one. Do these look sufficient to you?
Also, there appears to be no standard for coverage definition: so by "50X" I intend exome-wise coverage of 100bp uniquely-mapping Illumina paired reads, after duplicate removal.
Thanks!
Federico
I was wondering if there is a standard "coverage" for exomic SNP calling in tumor_vs_healthy samples (same patient). As we know, tumor samples have an intrinsically higher mutability (Parsons et al., 1993). I was thinking of applying a threshold of at least 20X for the healthy one, and 50X for the tumor one. Do these look sufficient to you?
Also, there appears to be no standard for coverage definition: so by "50X" I intend exome-wise coverage of 100bp uniquely-mapping Illumina paired reads, after duplicate removal.
Thanks!
Federico
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