Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.

i got this error message why

EarendilEarendil Posts: 2Member
edited January 2013 in Ask the GATK 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
Tagged:

Best Answer

Answers

Sign In or Register to comment.