Wilder B. Galvão wbgalvao
wbgalvao
/ hg38_to_hg19.py
Last active
August 14, 2020 18:07
Transform .bed files genomic coordinates from hg38 to hg19
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| import os | |
| import sys | |
| import pandas as pd | |
| from pyliftover import LiftOver | |
| target = sys.argv[1] |
wbgalvao
/ fix-multianno-header.sh
Created
August 13, 2020 18:10
Given a multianno file (annovar's output) fix its header by adding the vcf columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and SAMPLE)
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| #!/bin/bash | |
| multianno=${1} | |
| header=$(head -1 ${multianno}) | |
| fixedHeader=$(echo "${header}" \ | |
| | sed 's/Otherinfo/VCF_CHROM/' \ | |
| | awk '{print $0"\tVCF_POS\tVCF_ID\tVCF_REF\tVCF_ALT\tVCF_QUAL\tVCF_FILTER\tVCF_INFO\tVCF_FORMAT\tVCF_SAMPLE"}' \ | |
| ) |