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Error message when runing FreeBayes

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

software error snp alignment sequence
• 1,785 views • link
updated by WouterDeCoster WouterDeCoster • written by wangyunyang • wangyunyang

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.

• 0 views • link
written by Arup Ghosh Arup Ghosh

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?

• 0 views • link
written by wangyunyang • wangyunyang

1 answer

You need to define Read Groups in your bam file.

• 0 views • link
written by WouterDeCoster WouterDeCoster

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