UNKNOWN_SM in .bestsm files

[kiran girdhar]

I ran 212 chipseq samples to match with WGS vcf file

For some samples I am getting UNKNOWN_SM in first column. I still get matching WGS vcf id though. 

Can you help me with this? 

#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT

UNKNOWN_SM ALL 71701 871308 0 0.00 0.00000 0.00 0.00 NA NA 0.04989 0.00 0.00 NA NA 0.000 -nan -nan

[Hyun Min Kang]

What does the header of VCF say? Is the ID included in your VCF?

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