Does BWA-MEM 2 account for overlapping reads within the paired end data?

Does the variant calling is affected when we have some overlapping reads within the paired end reads? I am planning to use variant calling using GATK but I am mapping with Bwa-mem2

mapping calling variant reads

• 1,220 views • link

written 1.8 years ago by ayeraselvan •

1 answer

Yes, GATK variant calling understands that a base mismatch in overlapping reads from the same read pair is actually derived just from observation of the underlying molecule.

• 0 views • link

written 1.8 years ago by LChart

Thank you! Have a nice day :)

• 0 views • link

written 1.8 years ago by ayeraselvan •

More posts like this

What are the risque of keeping variants which read have low mapping quality?
written 1.5 years ago by lacb •

Hello, I have a pipeline to do variant calling and a some point there is the GATK `FilterMutectCalls` tool which annotate the variants, and some …
Overlapping reads, how do we counter them while variant calling, haplotype calling, does it affect …
written 1.8 years ago by ayeraselvan •

I have Illumina paired end reads. My plan is on to do the mapping to the reference, sort them, remove the duplicates and use GATK …
Seeking Advice on Multisample Variant Calling Pipeline with BWA-MEME and GATK DRAGEN Mode
written 2.0 years ago by George •

Hello everyone, I am in the process of building a pipeline for multisample variant calling and have some questions regarding tool usage and their safety. …
bwa-mem low mapping quality human genome
written 5.5 years ago by moustafa_abohawya •

I have whole genome sequencing paired end data that I am trying to map to the human genome primary sequence hg38. I mapped using bwa-mem …
BWA Mem -M flag (mark split hits) effect on structural variation calling
written 6.7 years ago by fwuffy

Does anyone know if BWA Mem -M flag (mark shorter split hits as secondary) will have a detrimental effect on structural variation calling using split …
BWA mapping parameters for DNA capture sequencing protocol
written 7.0 years ago by graeme.thorn

I want to map samples (70bp paired-end) to a 30-gene panel using BWA (mem). They were generated using a capture kit so should have few …
SNP calling using samtools
written 7.6 years ago by ankit hinsu •

Hi all, I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand …
Paired end reads merged to single end for mapping - should i allow multi-overlap similar to paired …
written 8.7 years ago by devikaparvathy •

I am using featurecounts after mapping of my reads. I have a paired-end sequencing data but Only a low percentage of reads were mapped when …
Assembly: collapsed reads vs overlapping paired-end reads?
written 9.9 years ago by palu •

Hello all! **Case:** We did a Sequencing of three yeast strains (not s.cerevisiae) and with reference genome available! Illumnia MiSeq around 8,5 million reads each …
Paired-End Reads Alignment For Variant Calling ?
written 13.1 years ago by newDNASeqer

<p>I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use …