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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

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2 hours ago
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2nelly220



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