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molgenis / vip

Variant Interpretation Pipeline
https://molgenis.github.io/vip/
GNU Lesser General Public License v3.0
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Error if .cram doesn't contain reads for a chunk #405

Closed dennishendriksen closed 1 year ago

dennishendriksen commented 1 year ago

Create HG001_chr22.cram from HG001.cram and use as VIP input results in:

  [WARNING] Contig name chr1 provided but no mapped reads in BAM, skip!
  [WARNING] No mapped reads support in BAM for provided contigs set chr1
  [WARNING] No contig intersection found, output header only in merge_output.vcf.gz
  Command error:[W::hts_itr_multi_cram] No index entry for region 0:0-248956422
  mv: cannot stat ‘merge_output.gvcf.gz’: No such file or directory