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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:
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?