Results for "Depth"
Bio-Scripts
# get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 #...2212 days ago
- ...Analysis: Tools that count coverage, e.g. depth per allele ASEReadCounte...bam) with pair orientation fields (e.g. F1R2 ). AnnotateVcfWithBamDepth (Interna...
2077 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2057 days ago
Generate simulated polyploid genome !
...t both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads --depth 50 toyheterozygous3percent.fa...2055 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 >...
2006 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) >...
1606 days ago
Samtools commands for bioinformatician !
...sorted.bam.bam sal_ref_sej.fasta ### results into txt file samtools depth /path/to/sorted_bam.bam > /path/to/coverage_results.txt ### note: returns count of depth at each position. input shoul...1605 days ago
Tadpole is 250x faster than SPADes assembler !
...Only dump kmers with at least this depth. showstats=t Print a...to ignore kmers with depth of that value or lower. preh...ratio of 1st to 2nd-greatest path depth at low depth. branchlower=3...his means they have no kmers above depth 1 (2 for paired...978 days ago
