We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
The number of variants after hard-filter increased from the number of variants without hard-filter
How do I have more variants after hard-filtering than before hard-filtering?
Variant Call without hard-filtering:
~/gatk-220.127.116.11/gatk HaplotypeCaller -R Reference_genome.fasta -I KMM2_bwamem_alignment_samblaster_samtoolsview_samtoolssort_09292018.bam -O KMM2_raw_snps_indels_annotations_09302018.vcf -A BaseQualityRankSumTest -A FisherStrand -A MappingQu alityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A StrandOddsRatio -A InbreedingCoeff
(gatk) [[email protected] KMM2_analysis]$ grep -v '#' KMM2_raw_snps_indels_annotations_09302018.vcf | wc -l
Variant Call with hard-filtering (snps):
~/gatk-18.104.22.168/gatk VariantFiltration -R Reference_genome.fasta -V KMM2_raw_snps_indels_annotations_09302018.vcf -filter "QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filter-name "snpfilter1" -O KMM2_filtered_snps_snpfilter1_10012018.vcf
Variant Call with hard-filtering (indels):
~/gatk-22.214.171.124/gatk VariantFiltration -R Reference_genome.fasta -V KMM2_raw_snps_indels_annotations_09302018.vcf -filter "QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filter-name "indfilter1" -O KMM2_filtered_indels_indfilter1_10012018.vcf
Merging hard-filtered snps and indels
picard MergeVcfs I=KMM2_filtered_snps_snpfilter1_10012018.vcf I=KMM2_filtered_indels_indfilter1_10012018.vcf O=KMM2_combined_filtered_variants_filter1_10012018.vcf
[[email protected] KMM2_analysis]$ grep 'PASS' KMM2_combined_filtered_variants_filter1_10012018.vcf | wc -l