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IndelRealigner losing some reads
Recently I experienced a slightly annoying problem with IndelRealigner loosing some reads. It is usually just few reads missing from the output, but when I compare the output and input and extract the reads taht are missing after the IndelRealigner job, I cannot see what is wrong with them. An example of one such read is below:
M01823:187:000000000-AB050:1:1109:16397:19623 69 8 64405501 0 * = 64405501 0 TTTGCTTTCAAAAATACCTGTGCAGGTGGAGGTGTGCGTCTGCGTCTAACGGTGTGCGGTGCGAATTTCGACGATCGTTGCATTAACTTGCGAAACCCCTCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAATAAAACAAACAAAACGAACTACTACAGACAACGACAAAAACCAAAAAACAACATATAAACAAATAAACGAGCAACACAACACAAATAAAAGAGCAAGCACTACAC CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG885+3355<,8,,=,,,,,,3,,=4::?,,7,,7,*2+14<********/*/2***1/*0+++2++2/+++++*2*12*2*****2*;*/++2+++1:68***20++++* RG:Z:140919_M01823_0188_000000000-AB050_AACCCCTC-TGTTCTCT_L001 AS:i:0 XS:i:0
It's pair has been kept, but this read was removed.
It is a bit of nuisance, as in our workflow we check the number of reads in the files after various steps for sanity, so varying number of reads introduces problems. I would be grateful if you could adviice why some reads get ommitted by IndelRealigner so I could modufy our workflow accordingly. Or could it be a bug?