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, 08:34, 18 May 2012
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| # SEQ_SM : Sample ID of the sequenced sample. Obtained from @RG header / SM tag in the BAM file | | # SEQ_SM : Sample ID of the sequenced sample. Obtained from @RG header / SM tag in the BAM file |
| # RG : ReadGroup ID of sequenced lane. For [outPrefix].selfSM and [outPrefix].bestSM, these values are "ALL" | | # RG : ReadGroup ID of sequenced lane. For [outPrefix].selfSM and [outPrefix].bestSM, these values are "ALL" |
− | * CHIP_ID : Sample ID compared to in the genotype file. For [outPrefix].selfRG and [outPrefix].selfSM, these values should be identical to [SEQ_SM] or "NA" if the genotype of sequenced samples are unavailable. For [outPrefix].bestRG and [outPrefix].bestSM, these values should be the ID of best-matching sample among the genotype files compared to.
| + | # CHIP_ID : Sample ID compared to in the genotype file. For [outPrefix].selfRG and [outPrefix].selfSM, these values should be identical to [SEQ_SM] or "NA" if the genotype of sequenced samples are unavailable. For [outPrefix].bestRG and [outPrefix].bestSM, these values should be the ID of best-matching sample among the genotype files compared to. |
| # # SNPs : # of SNPs passing the criteria from the VCF file | | # # SNPs : # of SNPs passing the criteria from the VCF file |
| # # READS : Total # of reads loaded from the BAM file | | # # READS : Total # of reads loaded from the BAM file |