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Question: GATK HaplotypeCaller Problems
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Recently I used GATK4 to calling variations with the HaplotypeCaller and the bam file that HC produced during reassembly has been required to output using this command guided by GATK instructions. java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R human_b37_20.fasta -I recalibrated.bam -o hc_variants.vcf -bamout bamout.bam Then I found the hc_variants.vcf that has been produced together differs from the gatk4_all.vcf. Therefore, I want to ask if there exists some differences when the -bamout argument has been used and what does the hc_variants.vcf tries to interpret?

ADD COMMENTlink 11 months ago chengye • 10 • updated 10 months ago Biostar 20
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what is gatk4_all.vcf ???

https://commons.wikimedia.org/wiki/Category:Crystal_balls#/media/File:Paulinefrederick_5_retouched.jpg

ADD REPLYlink 11 months ago
Pierre Lindenbaum
120k
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It's one file that GATK4 outputs like 19B0117126-1_gatk4_all.vcf while the prefix is the sample ID.

ADD REPLYlink 11 months ago
chengye
• 10
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2

I'm suprised you speak about gatk4.0 which should look like:

gatk   HaplotypeCaller   -R Homo_sapiens_assembly38.fasta ...

while the syntax

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller

looks like gatk 3.8 ...

ADD REPLYlink 11 months ago
Pierre Lindenbaum
120k
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I feel sorry to explain that the command I supplied is just a simple copy from the GATK website while the command I used is below /ifs4/HST_5B/USERS/cuixiaoli/Software/jdk1.8.0_144/bin/java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /ifs4/HST_5B/USERS/cuixiaoli/Software/gatk/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar HaplotypeCaller -R /ifs7/B2C_SGD/PROJECT/PP12_Project/analysis_pipeline/HPC_chip/db/aln_db/hg19/hg19_chM_male_mask.fa -L $bed -I /ifs7/B2C_SGD/PROJECT/MGISEQ-2000_Project/v23_tumor171/tumor171_LCY19SZ000027_20190205_11/19B0118580/bwa/19B0118580.final.bam -O /ifs7/B2C_USER/chengye/gatk3_cmp_gatk4/gatk41_cmp_31_unfiltered/19B0118580/hc_variants_bed_sup.vcf -bamout /ifs7/B2C_USER/chengye/gatk3_cmp_gatk4/gatk41_cmp_31_unfiltered/19B0118580/bamout_bed_sup.bam

ADD REPLYlink 11 months ago
chengye
• 10

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