Results for "Samtools"
Bio-Scripts
#!/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 > c...2005 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....2005 days ago
Setting up falconUnzip conda environments for genome assembly !
...ge readline: 7.0-haf1bffa_1 conda-forge requests: 2.20.1-py27_1000 conda-forge samtools: 1.9-h8ee4bcc_...1991 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
1835 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) >= 3){$c++;}}...
1605 days ago
Samtools commands for bioinformatician !
...sam # -o : output file name samtools view -b -S -o sal_sej.bam sal...# -f INT show flag matches samtools -f 4 sal_sej.bam | less #...# always index sorted files samtools index sal_sej_sorted.bam.bam...### results into txt file samtools depth /path/to/sorted_bam.bam...1604 days ago
Bash script to alignment of short reads against reference genome !
...413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam...nd file the second mate. #conversion to BAM: samtools view -b - --- this reads SAM...549_1.fastq.gz SRR341549_2.fastq.gz \ | samtools view -b - >SRR341549.raw.mini...1560 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
...a-dev cd /usr/bin wget https://github.com/samtools/htslib/releases/download/1.9/...b-1.9 make cd .. wget https://github.com/samtools/samtools/releases/download/1....in/bcftools-1.9" export PATH="$PATH:/usr/bin/samtools-1.9" export PATH="$PATH:/usr...1559 days ago
Bash command to install bwa, samtools, picard !
...g transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install samtools Collecting package metadata...rkshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - samtools The following packages w...1556 days ago
To convert just one specific read group to fastq
...PLE_{} QUIET=true 2>> log.txt" # Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam...igate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" e...1543 days ago
