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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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"Parameter required for id", resolved by manually inserting id fields in `-sr` arguments #114

Open evanbiederstedt opened 7 years ago

evanbiederstedt commented 7 years ago

Previous issues have dealt with the error "Parameter required for id" with respect to Lumpy:

https://github.com/arq5x/lumpy-sv/issues/82)

For this case, previously resolutions will not solve this issue, i.e.

(1) the BAMs are coordinate-sorted (2) this is not an awk/gawk issue (3) readgroups have SG, ID, and LB information

For this issue, there appears to be a parsing error upstream, i.e. the -pe flag has the id information but the -sr flags do not; the id: fields are empty. The current resolution is for users to manually insert id: fields into each -sr argument when calling lumpy.

ernfrid commented 7 years ago

Can you attach a copy of the header of your BAM and provide the output from running lumpyexpress with the -v option on?