Tag: sambamba

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ？, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

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Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

Strange speed up in GATK LeftAlignIndels 1 Hi! I noticed a strange thing, I have been running a DNA-seq pipeline like this: reads -> bwa-mem2 -> picard SortSam -> picard MergeSamFiles -> picard MarkDuplicates -> gatk LeftAlignIndels … gatk LeftAlignIndels has always taken around 4 hours to complete with the…

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Sambamba markdup usage help 0 Hi! I need so help regarding the usage of sambamba markdup. I have read the documentation but I don’t quite understand. What is meant by insert size here? –hash-table-size=HASH_TABLE_SIZE size of hash table for finding read pairs (default is 262144 reads); will be rounded down…

Sambamba 1 Hi can anyone guide me how to install sambamba package in ubuntu 20.04 install sambamba ubuntu • 22 views The documentation for getting binary (64bit linux) packages and compiling this software from source is found on the home page of the package: lomereiter.github.io/sambamba/ If you need more help…