Results for "vcf"
Bio-Scripts
Create random 1000 INDEL in genome !
...mulation: simuINDEL.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuINDEL.refseq2simseq.INDEL.vcf [Sun Jan 10 16:14:00 2021]...1215 days ago
Create random 1000 CNVs in genome !
...simulation: simuCNV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuCNV.refseq2simseq.CNV.vcf [Sun Jan 10 16:24:20 2021]...1215 days ago
Create random 5 inversions in genome !
...simulation: simuINV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuINV.refseq2simseq.inversion.vcf [Sun Jan 10 16:30:40 2021]...1215 days ago
Create random 2 translocations in genome !
...mulation: simuTRANS.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuTRANS.refseq2simseq.translocation.vcf [Sun Jan 10 17:12:58 2021]...1215 days ago
Corona variant calling steps !
...-p results/sam results/bam results/bcf results/vcf bwa mem trimmed_fastq_small...call --ploidy 1 -m -v -o results/bcf/$basename.vcf results/bcf/$basename.bcf v...t_Results_of_COVID_gz" rem cp -r results/bcf/*.vcf.gz Variant_Results_of_COVID_g...1049 days ago
Bash script to simulate a genome !
...bbmap/ /genetics/elbers/bbmap-38.86/mutate.sh \ in=GCA_003401745.1_ASM340174v1_genomic.fna_upper.fasta.gz \ ow=t \ vcf=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.vcf.gz \ out=GCA_003401745.1_ASM...922 days ago
Perl script to parse VCF file !
...se strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl...ss @ARGV; my $vcf_file = shift @ARGV; my @vcf_entries = parse_vcf($vcf_file..."; my %chromosome_counts; for my $entry (@vcf_entries) { $chromosome_c...98 days ago
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