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.

i got this error message why

EarendilEarendil Posts: 2Member
edited January 2013 in Ask the team

ERROR MESSAGE: SAM/BAM file genome_110616_SN365_A_s_7_seq_GQJ-1.pe.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups

i am very new to GATK and i was trying to invoke the readcount command and i got the error above what is read groups.

thank you

Post edited by Geraldine_VdAuwera on
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