Chromosome blocks not continuous error in cram workflow

molgenis / vip

Variant Interpretation Pipeline

https://molgenis.github.io/vip/

GNU Lesser General Public License v3.0

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Chromosome blocks not continuous error in cram workflow #417

Closed bartcharbon closed 1 year ago

bartcharbon commented 1 year ago



&&

[E::sam_index] Read 'A0379:759:HNH3DSX3:1:2141:2701:26772' with ref_name='chr1_KI2072v1_random', ref_length=176043, flags=163, pos=2028 cannot be indexed

samtools index: failed to create index for "vip_fam26_.cram.bam"```

dennishendriksen commented 1 year ago

duplicate, see https://github.com/molgenis/vip/issues/431