Open jdselwyn opened 5 years ago
Need to update instructions because first column of pop.map file returns entire column name and the cnv file doesn't need the cutoffs.
popmap file: FCOP-1_GAGTGG_L004.1.1-RG.bam FCOP-1 FCOP-2_GATCAG_L004.1.1-RG.bam FCOP-2 FMAT-1_GTTTCG_L004.1.1-RG.bam FMAT-1 FMAT-2_GTGGCC_L004.1.1-RG.bam FMAT-2 FSAN-1_TAGCTT_L004.1.1-RG.bam FSAN-1 FSAN-2_GGCTAC_L004.1.1-RG.bam FSAN-2
CNV file: FCOP-1_GAGTGG_L004 10 FCOP-2_GATCAG_L004 10 FMAT-1_GTTTCG_L004 10 FMAT-2_GTGGCC_L004 9 FSAN-1_TAGCTT_L004 10 FSAN-2_GGCTAC_L004 9
I updated the config.4.all, leaving this open for now until I figure out exactly why this difference is necessary.
config.4.all
Need to update instructions because first column of pop.map file returns entire column name and the cnv file doesn't need the cutoffs.
popmap file: FCOP-1_GAGTGG_L004.1.1-RG.bam FCOP-1 FCOP-2_GATCAG_L004.1.1-RG.bam FCOP-2 FMAT-1_GTTTCG_L004.1.1-RG.bam FMAT-1 FMAT-2_GTGGCC_L004.1.1-RG.bam FMAT-2 FSAN-1_TAGCTT_L004.1.1-RG.bam FSAN-1 FSAN-2_GGCTAC_L004.1.1-RG.bam FSAN-2
CNV file: FCOP-1_GAGTGG_L004 10 FCOP-2_GATCAG_L004 10 FMAT-1_GTTTCG_L004 10 FMAT-2_GTGGCC_L004 9 FSAN-1_TAGCTT_L004 10 FSAN-2_GGCTAC_L004 9