freebayes issue for BAM file

Question

[shangzhenhua08]

Hi, I am doing variant allele discovery via freebayes. However, I always got Opened BAM reader without index file, jumping is disabled. could not find SM: in @RG tag @RG ID:FASTQ_Groomer_on_data_1. Can anybody help me to figure it out?

Answer 1

[Pierre Lindenbaum]

The message is clear: your BAM header is missing a sample name (SM) in the read group (RG) see :

Read Group In Sam/Bam Files: What Do They Exactly Describe?

Adding Read Groups To Bam Files