add --rg_sample for SNP calling

[Hu Wang]

Hi Brian,

Just wonder do you have any example format for adding rg_sample for variant calling for "${TRINITY_HOME}/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py"

I was calling SNPs for multiple samples, but found only all the samples were merged together as one sample in the output.vcf. I think this could be caused by missing RG_SAMPLE, correct?

More specifically, is the order of -- rg_sample same as the one for -S SAMPLES_FILE?

Super thanks in advance,

Hu

[Brian Haas]

Hi,

This pipeline assumes a single sample, for which you potentially have multiple sets of reads.  If you have multiple samples each with different variant profiles, you'll want to run this separately for each of them and get separate vcfs.

hope this helps,

Brian

[Janay Fox]

Ohhh I realize now I did the same thing since I thought the -S option would indicate sample files for multiple samples. So even with the -S option with a sample file that specifies the different treatment groups of samples you would need to run separately for each sample?