Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.
can I use
samtools index to index reduced bam files? I'm using GATK version 2.7-2-g6bda569 and HC asks for the index files.
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