Question: Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
gravatar for Susmita Mandal
8 days ago by
Susmita Mandal40 wrote:

Hello everyone,

I am running HaplotypeCaller by GATK for variant calling and I'm getting only indels and no SNPs. I happen to know that the sample contains SNPs as I'm reproducing the data from another paper. Following is the code that I'm following. Let me know where I'm making a mistake or there is some other reason behind this.

STAR --runThreadN 10 --genomeDir /home2/NEW_ANALYSIS/X-chromosome/Star_Indexed --readFilesCommand zcat --readFilesIn SRRXXXXXXX.fastq.gz --outFilterMismatchNmax 0 --outFilterMultimapNmax 1 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --outFileNamePrefix SRRXXXXXXX_

java -jar picard.jar MarkDuplicates I=SRRXXXXXXX_Aligned.sortedByCoord.out.bam O=SRRXXXXXXX_Aligned.sortedByCoord_dup_marked.bam M=SRRXXXXXXX_marked_dup_metrics.txt

java -jar picard.jar AddOrReplaceReadGroups I=SRRXXXXXXX_Aligned.sortedByCoord_dup_marked.bam O=SRRXXXXXXX_Aligned.sortedByCoord_dup_marked_RGadded.bam RGID=SRRXXXXXXX RGSM=SRRXXXXXXX RGPU=SRRXXXXXXX RGLB=SRRXXXXXXX RGPL=illumina SORT_ORDER=coordinate CREATE_INDEX=True

java -jar GenomeAnalysisTK.jar -R GRCh38.fa -T HaplotypeCaller -I SRRXXXXXXX_Aligned.sortedByCoord_dup_marked_RGadded.bam --dbsnp dbsnp.vcf -U ALLOW_N_CIGAR_READS -o SRRXXXXXXX_HaplotypeCaller.out.raw.snps.indels.vcf



ADD COMMENTlink modified 8 days ago • written 8 days ago by Susmita Mandal40
gravatar for Pierre Lindenbaum
8 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:
 --outFilterMismatchNmax 0

as far as I understand, you don't allow any mismatch, hence you get no SNV.

ADD COMMENTlink written 8 days ago by Pierre Lindenbaum120k

I have gotten SNVs using this option previously.

ADD REPLYlink written 8 days ago by Susmita Mandal40

is there any read with NM>0 , what is the mean MAPQ ? what is the mean depth ? do you know any position of a known SNV ? do you see it with IGV ? what is the depth/MAPQ ? etc...

ADD REPLYlink written 8 days ago by Pierre Lindenbaum120k

I got SNPs after removing --outFilterMismatchNmax 0 in my mapping step!

ADD REPLYlink written 7 days ago by Susmita Mandal40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1504 users visited in the last hour