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chmod a+x vcfsort.sh | |
vcfsort.sh trio.trim.vep.vcf.gz |
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grep -v "^@" $1 | awk '{print $1"\t"$2"\t"$3"\t"$5}' > $(dirname $1)/$(basename $1 .interval_list).bed && \ | |
bgzip $(dirname $1)/$(basename $1 .interval_list).bed && \ | |
tabix $(dirname $1)/$(basename $1 .interval_list).bed.gz |
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first_reads=$1 | |
second_reads=$2 | |
ddir=$(dirname $first_reads) | |
obase_first=$(basename $first_reads .fastq.gz) | |
obase_second=$(basename $second_reads .fastq.gz) | |
splitsz=4000000 | |
if [ ! -z ${first_reads} ] && [ -e ${first_reads} ] |
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import sys | |
import gzip | |
from collections import defaultdict | |
if __name__ == "__main__": | |
d_telo= defaultdict(list) | |
d_centro = {} | |
with gzip.open(sys.argv[1], "rt") as ifi: | |
for line in ifi: |
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git clean -xfd | |
git submodule foreach --recursive git clean -xfd | |
git reset --hard | |
git submodule foreach --recursive git reset --hard | |
git submodule update --init --recursive |
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library(vcfR) | |
# Import VCF | |
my.vcf <- read.vcfR('my.vcf.gz') | |
# Combine CHROM thru FILTER cols + INFO cols | |
my.vcf.df <- cbind(as.data.frame(getFIX(my.vcf)), INFO2df(my.vcf)) |
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