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filter_indels.pl vcf2 error #294

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alkc opened this issue Feb 7, 2025 · 0 comments
Open

filter_indels.pl vcf2 error #294

alkc opened this issue Feb 7, 2025 · 0 comments

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@alkc
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alkc commented Feb 7, 2025

found in indel_vep .command.login production:

Can't exec "file": Permission denied at /fs1/pipelines/pipeeval/repos/cmd_wgs/bin/vcf2.pm line 286.
Use of uninitialized value $file_str in pattern match (m//) at /fs1/pipelines/pipeeval/repos/cmd_wgs/bin/vcf2.pm line 287.

occurs in filters_indels.pl

haven't checked if it breaks filtering in any way. filtering of indels still seems to occur.
@alkc alkc mentioned this issue Feb 7, 2025
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