2 hours ago by
Geneva,Switzerland
Hi all,
I was given a bam file to process for variant calling. However GATK gives CIGAR error.
Checking the respective aligned reads I noticed a very strange possible error.
Do you have any idea what can cause this misconception with the CIGAR string after alignment with bowtie?
A00129:298:H7JGHDSXX:1:1105:9109:27853 147 19 4511282 60 150S = 4511317 -294 GGTGACCCCACTGCAGACAGTGTCCTTGGTACCGGTCAGCACGGTCTTGGCCGTGTCTACACCCGTCTGGACGGCCCCCTTGGCCACATTCGCAGCACCGGTCACCCCACTGCAGACGGTGTCCTTGGTACCAGTTAGGACAGTCTTGGT FFFFFFFF:FFFFFFFFF:FF:F:FFFFFFFFFF:FFFFFF:F,F,F:FF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:64A49C2A1C0A16A0C11 AS:i:115 XS:i:73 ra:i:1 cl:i:0
A00129:298:H7JGHDSXX:1:1105:9109:27853 99 19 4511317 60 150M = 4511461 294 GTCCAGGCCCCCCTGGACGGCCCCTTTGGCCACATTCGCAGCACCGGTCACCCCACTGCCAAGGGTGTTCTTTGTACCTGTTGCGATATTTTGGGTCGTTTTCAGCCCAGTTTGCACAGCACCCTTGGCCACGTTCACAGCACCGGTGAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFFFFFFF:FFF:FFFFFF:FFFFF NM:i:2 MD:Z:33T102G13 AS:i:140 XS:i:49 na:i:1 cl:i:2
How is it possible to get 150S in CIGAR string? The whole read is soft clipped but aligned!!!! This is bizarre.
Unless the file is modified.
Any suggestions?
Thank you
