which is good haplotypecaller and UnifiedGenotyper?
1
0
Entering edit mode
6.9 years ago
misbahabas ▴ 70

Asslamu Alikum

I am new user of GATK tool.

I successfully generated vcf file by GATK using follow ing command

java -jar GenomeAnalysisTK.jar -R /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/misbah_test_folder/DQ1_annotation/ucsc_canfam3/canFam3.fa -T UnifiedGenotyper -maxAltAlleles 15 -I /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/dog_bamfiles/dq1_bam_test/chr1.bam -o /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/misbah_test_folder/DQ1_annotation/ucsc_canfam3/unified_output.raw.snps.indels.g.vcf"

I used this vcf file for further annotation by snpeff. but now I am confused between haplotypecaller and UnifiedGenotyper. which is best one. Kindly tell me which one is good for this purpose

snp vcf next-gen • 3.1k views
ADD COMMENT
1
Entering edit mode

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1]

ADD REPLY
1
Entering edit mode
6.9 years ago

but now I am confused between haplotypecaller and UnifiedGenotyper. which is best one. Kindly tell me which one is good for this purpose

https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php

This (UnifiedGenotyper) tool has been deprecated in favor of HaplotypeCaller, a much more sophisticated variant caller that produces much better calls, especially on indels, and includes features that allow it to scale to much larger cohort sizes.

ADD COMMENT

Login before adding your answer.

Traffic: 2042 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6