FAQ: Output

SAM tags

Read group

• Picard is complaining about missing read group tags.

Variation and WASP

• What is the meaning of vW:i:N tags for WASP filtering?

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Variation and WASP

Q: What is the meaning of vW:i:N tags for WASP filtering?

The WASP tags vW are described in the manual, Chapter 11 "WASP filtering of allele specific alignments."

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Read group

Q: Picard is complaining about missing read group tags.

Read groups do not have to be present in the SAM/BAM file, and STAR does not add them by default. Picard requires them by default, which causes the error you see. I believe you can suppress Picard errors with IGNORE={MISSING_READ_GROUP,RECORD_MISSING_READ_GROUP} - please check the Picard manual for more options: http://broadinstitute.github.io/picard/command-line-overview.html
If you want to include read groups in STAR BAMs, you can use --outSAMattrRGline ID:my-read-group option.
You can also add RG tags to an existing BAM with samtools addreplacerg