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Results for "
samtools
"
Wire posts
Jit
@jit.aber
SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-
SamTools
/lib/Bio/DB/Sam.pm # Perl #SAM #BAM
2624 days ago
Jit
@jit.aber
samtools
view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam
2296 days ago
Neelam Jha
@neelam
Generate consensus from BAM file
samtools
mpileup -uf chr5B_leaf_rust.fasta M27454_5B_reads_sorted.bam | bcftools call -c | vcfutils.pl vcf2fq #BAM #Consensus
2034 days ago
Jit
@jit.aber
Extract sequence by ids $ xargs
samtools
faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences
1967 days ago
Jit
@jit.aber
samtools
mpileup -uf reference.nt mapping.bam | bcftools call -c | vcfutils.pl vcf2fq > consensus.fasta #Genome #Assembly #Reference
1919 days ago
Jit
@jit.aber
samtools
view -Sb pilonCor_round1.fasta.out.sam |
samtools
sort -m 4G -@ 40 -o pilonCor_round1.fasta.out.sorted.bam - &&
samtools
index -@ 40 pilonCor_round1.fasta.out.sorted.bam #SAM2BAM
1917 days ago
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