UnifiedGenotyper- problem when calling in chunks on reduced BAMs
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Hello,

Im trying to call variants using UnifiedGenotyper on ca 450 reduced bams in 100000 bp chunks. It works fine for some of the chunks, but for others I get the following error message:

ERROR MESSAGE: SAM/BAM nameOfBam.bam is malformed: Unexpected compressed block length: 1

Can anyone explain to me why there is a problem with a specific bam file when I call on for example chunk chr20:25400000-25500000 but not when I call on chunk chr20:10000000-10100000?

Thank you, Tota


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