Error message when runing FreeBayes

Question

[wangyunyang]

Dear all,

I got an error message when I was trying to call variants by using FreeBayes. The error message is:

ERROR(freebayes): could not find SM: in @RG tag @RG ID:Unpaired_reads_assembled_against_24353_tag_g20871 SM:

What does RG tag mean? How can I fix this error?

Thanks, Yunyang

[Arup Ghosh]

Check if Read Group already present in your bam file using samtools view -H |grep "@RG" . If RG is absent using Picard you can add them.

[wangyunyang]

Hi Arup,

Thanks for your reply. This is how my RG looks like:

@RG ID:Unpaired_reads_assembled_against_24353_tag_g20871 SM: @RG ID:Paired_Group_1_assembled_against_24353_tag_g20871 PI:296 SM:

Is there anything wrong?

Answer 1

[WouterDeCoster]

You need to define Read Groups in your bam file.