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ferrannadeu / IgCaller

Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in lymphoid neoplasms.
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samtools view -F 3328 excludes split-read support for translocation #4

Closed jbalberge closed 3 years ago

jbalberge commented 3 years ago

Hi Ferran It looks like Ig translocations are only supported by few split reads since some would be excluded with samtools view -F 3328 (x100 and x800 flags for supplementary/secondary alignments with bwa mem ±M). It seems a bit rough to me, is there any reason to exclude split read / mate pair support from translocation scoring? JB

ferrannadeu commented 3 years ago

Hi @jbalberge,

Thank you for your comment! No, there was not any reason to exclude split read/mate pair support from translocation scoring. This issue has already been fixed and will be available in the new version of the program. I will let you know once it is updated here (just doing the last checks).

Best,

Ferran

ferrannadeu commented 3 years ago

The updated version should solve this issue. Please, open it again if you think that it is not the case. Thanks for your input!