Results for "Bam"
Bio-Scripts
...0k-sv2.2/ref1.fasta greg200k-sv2.2/ref2.fasta greg200k-sv2.2/subreads1.bam 12 18.6M 12 2480k 0...0 517k 0 0:00:36 0:00:04 0:00:32 517kgreg200k-sv2.2/subreads1.bam.pbi greg200k-sv2.2/subreads1...2048 days ago
- ...1.9/test/md.fa htslib-1.9/test/md.fa.fai htslib-1.9/test/noroundtrip-out.vcf htslib-1.9/test/noroundtrip.vcf htslib-1.9/test/range.bam htslib-1.9/test/range.bam.bai htslib-1.9/test/range.cr...
2033 days ago
- #!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {print $0}' deduped_MA605.coverage...
2018 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i....2018 days ago
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1848 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(){chomp; @s = split(/\t/); if(scalar(@s)...
1619 days ago
Samtools commands for bioinformatician !
...amtools view -b -S -o sal_sej.bam sal_sej.sam ### viewing ba...atches samtools -F 4 sal_sej.bam | less ### count reads (..._ref_sej.fasta sal_sej_sorted.bam.bam > sal_vars.bcf ### c...ls depth -a sorted_dupremoved.bam | awk '{c++; if($3>0) total+=...1617 days ago
Bash script to alignment of short reads against reference genome !
...gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam sa...e second file the second mate. #conversion to BAM: samtools view -b - --- this...| samtools view -b - >SRR341549.raw.minimap2.bam sambamba sort SRR341549.raw....1573 days ago
To convert just one specific read group to fastq
...-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM...roups to paired files. samtools fastq -t -1 all1.fq -2 all2.fq all.bam # To convert just one spec...1556 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $...1351 days ago
