Entering edit mode
9.1 years ago
Stephanie
•
0
Hi all, I am using BWA mem on samples that have been sequencend on an Illumina HiSeq2500 in paired-end 2*125 nuclotides. I have not change any default option.So, in the results, I was expecting not to have any read with AS tag lower than 30, as this is the default value for -T option. The fact is that I have many reads with AS lower than 30 (most of them are 19, 20 or 21). These low alignment scores coincide with reads having a lot of soft-clipped sequences. Below is an example of read like that in my results: HWI-D00562:34:C6KW3ANXX:5:2205:14887:84822 99 chr12 71309226 40 17S19M89S = 7130922619 CCAATGAACCATATCAGTATTCCTGTGTCTCTTAAGCCACCTTATCACCCCTGTTGATATAGCAATGTGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGEGGGGGGGGGGGGGGGGG<CEEGGGGG<EGGGEGGGGGG..<FGGGGGGGGG MD:Z:19 PG:Z:MarkDuplicates NM:i:0 MQ:i:40 AS:i:19 XS:i:0 HWI-D00562:34:C6KW3ANXX:5:2205:14887:84822 147 chr12 71309226 40 73S19M33S = 71309226-19 CACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCAATGAACCATATCAGTATTCCTGTGTCTCTTAAGCCACCTTATCACCCCTGTTGATATAGCAATGTG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBCCCC MD:Z:19 PG:Z:MarkDuplicates NM:i:0 MQ:i:40 AS:i:19 XS:i:0 Why is this read pair reported in the output of BWA mem? It should have been discarded thanks to the -T 30 option, isn't it? How can I fix that? Thank you!
