VQSLOD score different for Full and split (by chromosome) BAM file

Dear all,

I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score:

For full : VQSLOD=-6.339e-01

For split : VQSLOD=-1.472e+00

Does this means splitting the BAM is not correct or is it because of wrong parameters? or it is correct and I can neglect this?

vcf gatk

• 1,570 views • link

updated 9.2 years ago by Biostar

• written 9.3 years ago by dasdevashishdas

0 answers

No answers yet.

More posts like this

transcript assembling problem by cufflinks
written 7.0 years ago by kuhelikadas1995 •

After alignment by hisat2 tool and generation of SAM ,BAM and sorted BAM files, I gave this command for transcripts assembling: cufflinks -o SRR1131119.sam -G …
How to split both bam files and annotation files as per chromosome number?
written 7.3 years ago by Glory Basumata

Hi All, I am working with a large output bam files generated from the STAR aligner. The alignment is done with hg38. I would like …
Why when splitting file in two we add 1 line before dividing the number of lines by 2?
written 8.0 years ago by salamandra

In [this tutorial][1] there's a part in which they try to shuffle the lines of a file and then split the file into two. I …
No QD scores on 10% of observations in VCF?
written 8.2 years ago by dthorbur

I am hard filtering my first VCF, and currently exploring the scores to set my thresholds. I'm basing this mostly on the GATK best practises …
Is there a tool to draw local ancestry plots per chromosome?
written 8.5 years ago by genomics Newbie •

Hello, Although this is a duplicate question from another posting, the previous post did not have any responses. Dear biostars: I'm doing local ancestry estimations …
Pindel error - malformed record detected
written 8.7 years ago by rooksie •

Hello, I have sam2pindel input files that are giving me a malformed record detected error. My command is: pindel -f ${refdir}/${refname} -p ${filename}_recal_output4Pindel.txt \ -c …
topTable in limma
written 8.8 years ago by AHW •

I am using limma to perform differential expression of illumina microarray gene expression data. I get the `topTable` by using the following line of code …
QUAL and AF GATK
written 10.5 years ago by aleka

Hi. I am a bit confused. I have my vcf files from GATK (exome data) and I want to filter out the low quality variants …
Is there a tool to draw local ancestry plots per chromosome?
written 10.7 years ago by bibb77

Dear biostars: I'm doing local ancestry estimations for GWAS data using the LAMP-LD software, I just got the results, which are ranges of ancestry across …
How Should I Split My Bams By Chromosomes ? For Which Operations ?
written 13.7 years ago by Pierre Lindenbaum

<p>On can split a <a href="http://www.biostars.org/p/50225/">BAM by chromosome</a> to speed up the processing of the BAMs.</p> <p>But it cannot be so simple: if two reads …