/ASE_PO

Primary LanguageShell

ASE

following WASP ##Mapping reads

  1. Map reads --> bam files (done by Darren) RNAseq 500HT Project

    • single end
    • hg19 (excluding 'random' chr)
    • BWA, less than 3 mismatches: bwa aln -n2
    • /group/ober-resources/resources/Hutterites/RNAseq_500HT/raw_data/

  2. SNPs in SNP directory

    • chr<#>.snps.txt.gz
    • position refallele altallele
    • awk -F"\t" '$4=="chr1" { print }' <file> > newfile

  3. to run WASP on all the reads (including remapping reads step) and put into output Directory :

    • Masterscript.sh <inputDir> <#jobspernode> <#Nodes> <outDir> <SNPDir>

###creating impute2 files

  1. impute2 haplotype file

    • plink --bfile /group/ober-resources/resources/Hutterites/PRIMAL/imputed-override3/imputed_cgi.po --geno 0.15 --keep PO_ids --missing --out phasedPO_g0.15_AD_gexppl --recode 12 --transpose where PO_ids contains parent of origin findivs

      • geno 0.15 : ~2.8M SNPs
      • geno 0.10 : ~ 1M SNPs

    • phased2imputehaps.pl

  2. impute2 genotype file

    • `plink
    • phased2impute.pl