Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller

Question

[Susmita Mandal]

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

Thanks

Susmita

Answer 1

[Pierre Lindenbaum]

 --outFilterMismatchNmax 0

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

[Susmita Mandal]

I have gotten SNVs using this option previously.

[Pierre Lindenbaum]

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...

[Susmita Mandal]

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