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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Bedtools Jaccard issue #113

Closed nvnieuwk closed 1 year ago

nvnieuwk commented 1 year ago

Description of the bug

  Error: Sorted input specified, but the file NA24149_DNA061747.g.vcf.gz has the following record with a different sort order than the genomeFile GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.fai
  chr14_GL000194v1_random   185 .   G   <NON_REF>   .   .   END=216 GT:DP:GQ:MIN_DP:PL  0/0:2:0:1:0,0,0

Command used and terminal output

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Relevant files

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System information

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