Bizarre CIGAR string
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
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are you using bowtie 1? The alignment is marking: Pair 1 is aligned in chr19:4511317, Pair 2 is not aligned but should be at 4511282. My suggestion is to align with BWA
Let s say that this is a task they gave me to do as a test. I know the potential solutions like convert back to fastq and realign. However, I suspect that this is a kind of pitfall they set me up on purpose. I just want to know what can cause this strange attitude apart from modifying the file on purpose. And yes it is bowtie1