Query regarding Haplotype Caller

Answered

Follow

Abrish

• February 15, 2022 20:22
• Edited

/home/anaconda3/share/gatk4-4.2.4.0-0/gatk HaplotypeCaller --java-options -Xmx100g -R genome.fa  -I fixed.bam -O NmMdAndUqTag_fixed.g.vcf.gz -ERC GVCF  --minimum-mapping-quality 20 --min-base-quality-score 20

 

In my case, We had used the Target enrichment sequencing approach for European Bison. We had sequenced a specific chromosome, for example, Chr1, Chr 2, Chr 15, Chr 9 for a specific gene panel. 

But When I check the results obtained using Haplotype Caller, I am getting variants (SNPs) for all chromosomes. I am very confused. Shouldn't We have Variant only on the specific Chromosome that I had mentioned above?  I was mainly interested to get Variant on specific sequenced (Mentioned above) chromosomes.

Do we have any specific program or parameter in GATK to call variants within targeted regions?

I had tried to use -L Haplotype caller parameter also. I had created a file named "interval_list", where I had mentioned the regions that were used to sequence. 

Chr "\t" Start Position "\t" End Position

But It didn't work for me. 

Your suggestions would be extremely helpful.

 

Thank you so much in advance. 

0

• 

  Abrish

  • March 12, 2022 22:53
  • Edited

  I would like to update regarding previous Query,

  I would like to mention once again that for target enrichment sequencing, we sequenced multiple specific regions of specific chromosomes. In my case, I had focused on chr12, 13, 15, 25. We had sequenced different specific regions related to specific genes for each chromosome. So Should I include these regions information also in this -L interval_list. Is It possible to include. As I am mainly intrested to see variants on these specific regions. 

  I have tried to perform like this , Is It a correct way?

  /home/anaconda3/share/gatk4-4.2.4.0-0/gatk HaplotypeCaller --java-options -Xmx100g -R genome.fa  -I fixed.bam -O fixed_25_1.g.vcf.gz -ERC GVCF  --minimum-mapping-quality 20 --min-base-quality-score 20  -L interval_list.bed

   head -n 3 interval_list.bed
  25 4088138 4103061
  25 5371120 6637687
  15 45220566 45250906

  First Column is Chromosome number.

   

  Interval_list.bed -> shows the specific regions on the specific chromosomes in which we are interested to see variants.

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • February 16, 2022 18:19

  Hi Abrish,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Non-Human topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • February 22, 2022 20:41

  Hi Abrish,

  Could you share the complete program log for your HaplotypeCaller command using the interval list bed file? The bed file format should work just fine. 

  I also noticed you are using --include-non-variant-sites which is an argument for GenotypeGVCFs and not HaplotypeCaller.

  Best,

  Genevieve

  0

  Comment actions Permalink
• 

  Abrish

  • March 12, 2022 23:04
  • Edited

  Dear Genevieve Brandt (she/her),

  Thank you so much.

  Here in the given link below, I have explained the same query in detail. 

  https://gatk.broadinstitute.org/hc/en-us/community/posts/4656472336283-Query-regarding-Intervals-and-interval-lists-for-Target-Enrichment-Sequecing

  Kindly help me regarding this. I would be extremely grateful. 

  Thank you so much in advance.

  0

  Comment actions Permalink

Please sign in to leave a comment.