Bizarre CIGAR string

Question

[2nelly]

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

[JC]

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

[2nelly]

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