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which is good haplotypecaller and UnifiedGenotyper?

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
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updated by Ram Ram • written by misbahabas • misbahabas

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updated by lakhujanivijay lakhujanivijay • written by WouterDeCoster WouterDeCoster

1 answer

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.

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written by Pierre Lindenbaum Pierre Lindenbaum

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