Joint variant calling

Hi,

I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 samples. I am going to use GATK and bcftools and then compare results. Bacteria are haploid. In the following commands, -ploidy must be set to 1 or 1500?

bcftools call -m -v --ploidy 1 -O z -o variant.vcf.gz mpileup.bcf

java -jar $GATK -T UnifiedGenotyper -R reference.fa -I bam.list -glm BOTH -stand_call_conf 30 -ploidy 1 -o call.vcf

joint variant calling

• 4,056 views • link

written 9.0 years ago by arash.iranzadeh1980 •

why you are not using HaplotypeCaller?

The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call indels is far superior, and it is now capable of calling non-diploid samples. As of GATK version

3.3, we recommend using HaplotypeCaller in all cases, with no exceptions.

--sample_ploidy / -ploidy

Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). Sample ploidy - equivalent to number of chromosome copies per pool. For pooled experiments this should be set to the number of samples in pool multiplied by individual sample ploidy.

• 0 views • link

written 9.0 years ago by Medhat

If you use the HaplotypeCaller, you should use --ploidy 1. I assume that for bcftools the logic should be similar

• 0 views • link

written 6.8 years ago by mgdias.jose •

0 answers

No answers yet.

More posts like this

bcftools parameter to define mitochondrial heteroplasmy and haploid condition.
written 5.5 years ago by bandanaschapagain •

Hi, I am trying to analyse my mitochondrial data set. As mitochondria are heteroplasmic and haploid, while using bcftools how can I specify both? Earlier …
SNP Calling using Genome Analysis Toolkit
written 5.8 years ago by Fid_o •

Greetings, I want to do SNP analysis (variant call) using the steps below which I got from https://approachedinthelimit.wordpress.com/2015/10/09/variant-calling-with-gatk/ These steps use short reads. But I …
bcftools for plant SNPs
written 5.8 years ago by Ric

Hi, I ran bcftools in the following way: bcftools mpileup -O b -o ${3}-${basename}.bcf -f $asm $bam bcftools call --ploidy 2 -m -o ${3}-${basename}.vcf ${3}-${basename}.bcf …
Variant calling and downstream analysis
written 9.1 years ago by arash.iranzadeh1980 •

Hi, I have whole genome sequencing data of 1605 bacterial samples in paired-end reads fastq format. These samples come from 3 phenotypes. I have also …
Produce raw SNP calls
written 10.1 years ago by cristina_sabiers

I will dance around my pc if get this last step XD I try call my snps with this code ``` java -Xmx4g -jar /home/cri/Desktop/GATK/GenomeAnalysisTK.jar …
How to improve the pipeline of call snp in RNA-seq?
written 10.1 years ago by liuhui •

Hi, Recently, I have tried to construct a pipeline (as the following lines show) to **call snp** after reading the workflow of [GATK][1] and [samtools][2] …
Why GATK and bcftools SNP calling different?
written 10.4 years ago by fernardo

Hi all, I am trying to find SNP/Indel in a dataset using both "*GATK*" and "*bcftools call*". I find two big differences for generating VCF …
VariantRecalibrator in GATK
written 11.3 years ago by 897598644

Excuse me: I used unifiedGenotyper in GATK to call variants and filterd variants with VQSR. There were errors: ``` java -jar GenomeAnalysisTK.jar \ -T ApplyRecalibration …
Can Some One Explain These Gatk Unifiedgenotyper Commands And Difference In Terms Of Output Also
written 12.9 years ago by always_learning

Can some one explain these GATK Unifiedgenotyper Commands and difference in terms of output also This one is basically used for calling Dindel target 1) …
Gatk Unifiedgenotyper
written 13.6 years ago by Biostar User •

Hi all, is GATK unifiedGenotyper call Indels ? I ran the following command line and got error! <pre><code>java -jar /software/GATK-1.0.5083/GenomeAnalysisTK.jar -l INFO -R …