scripts/do_star.sh

scripts/Snp_phased.v03.sh

--total SNPs:15,160,915

not in repeats

bedtools intersect -a hg38/dbsnp/dbSnp153Common.bed -b hg38/repeatMask/hg38.repeats.bed -v > SNPs/hg38_snp153_repeatmasker.bed

--6942367 SNPs left

not in imprinted genes (from geneimprint)

bedtools intersect -a SNPs/hg38_snp153_repeatmasker.bed -b hg38/imprinted_Genes/Impri.pos.bed -v > SNPs/hg38_snp153_rmi.bed

--6909945 SNPs left

main software: ncbi-igblast-1.15.0

scripts/do_mr.sh