UnifiedGenotyper- problem when calling in chunks on reduced BAMs
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?