How mutect treat paired end downsampled reads?
I have two question that are interrelated to each other.
I have two matched normal-tumor tissue WGS data. These data were mapped to reference genome using BWA. In the first pair the average coverage of the normal tissue is 100X and tumor tissue is 50X and in the second pair the average coverage of normal tissue if 80X and tumor tissue is 120X. To make data comparable I am downsampling normal tissue bam file in the first pair and tumor tissue bam file in the second pair using printRead. Then I am comparing the downsampled bam files together with matched original bam file to identify SNPs using Mutect. My question is :
1) During down sampling how printRead treat paired end reads if one read is mapped to the high coverage region and second in the low coverage region? Does it remove both or just the one in the high coverage region?
2) If the low coverage region read is not removed how Mutect treat unpaired read? Does it include the pseudo unpaired read in the analysis or discard ?