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FastQC before and after Base Quality Score Recalibration (BQSR)

gatk bqsr snp fastqc written 4 weeks ago by alicia.poppy • 40

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171

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GATK quality recalibration to get recalibrated BAM files before SNP calling

gatk bqsr recalibration snp written 5 weeks ago by alicia.poppy • 40 • updated 5 weeks ago by Nicolas Rosewick ♦ 7.9k

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Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files

bam sam sort markduplicates bqsr tool written 8 months ago by Charlotte.Herzeel • 140

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545

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error using bqsr and incompatible contigs

gatk bqsr written 11 months ago by bioguy24 • 190 • updated 6 months ago by Biostar ♦♦ 20

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259

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Adam Transform BQSR result is different with Gatk

gatk bqsr adam written 10 months ago by zhangnew • 0

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425

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multithread support for gatk

gatk bqsr written 11 months ago by bioguy24 • 190

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GATK4 BaseRecalibrator and Target region (whole exome data)

gatk4 bqsr written 13 months ago by oghzzang • 40

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BQSR: when it is applicable?

gatk bqsr base quality written 20 months ago by lamteva.vera • 160 • updated 20 months ago by finswimmer ♦ 11k

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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.

gatk bqsr freebayes written 2.3 years ago by sktbanerjee1 • 30 • updated 2.3 years ago by finswimmer ♦ 11k

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BamUtil for Base Qual Recalibration

gatk bqsr basequal recalibration recal written 4.6 years ago by Danielk • 570

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Recent Replies

A: How to make batch univariate cox analysis for list by Kevin Blighe ♦ 45k
My Bioconductor package, *RegParallel*, will do this for you, i.e., it can test each gene indepen...
C: Extract reads from a bam file to have two fastq files with the same number of re by genomax ♦ 69k
4596 + 0 singletons (0.08% : N/A) Some are explained by those.
C: Extract reads from a bam file to have two fastq files with the same number of re by macielrodriguez2 • 20
It worked great!!! Thank you so much genomax!!! But what are these reads? According to my flags...
C: Get Gene symbols by qicaibiology • 10
That is great if the author can help to make it through. I will shared my notes/process on each s...
A: Is it possible to directly convert fastq to CRAM ? by Charles Warden ♦ 7.0k
While some programs require uncompressed .fastq files, many/most will accept .fastq.gz files. Cr...
C: Is it possible to directly convert fastq to CRAM ? by genomax ♦ 69k
For reference [manual page][1] appears to say otherwise. Or should that additionally say "not req...
C: Get Gene symbols by jared.andrews07 • 2.7k
Yes, as I said, this will cause that error due to the duplicate row names. You need to figure out...
C: I want to know if there is reference for brain cell types by jared.andrews07 • 2.7k
There are about 9 billion different cell types in the brain, so that sounds like quite the task. ...
A: Is it possible to directly convert fastq to CRAM ? by jkbonfield • 120
While CRAM is indeed much smaller than BAM, its primary benefit is when using aligned data so you...
C: Pipe SamToFastq, BWA mem not working by ATpoint ♦ 19k
Ok, on Mac I sometimes had issues with non-writable stdout. As for the character limit, just add ...
C: Help making a blast database with longer sequence IDs by ravila • 0
Thanks! That solved the issue.
C: Augustus output (GFF file) to Anvi`o by Juke-34 • 2.2k
Do you use the option `—gff3` in Augustus? Because is you use the GTF output it is a bit wierd ...

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