Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

empty variant to table file

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3 comments

  • Avatar
    Bhanu Gandham

    Maybe its a transient error. Can you try again?

    Also please post the exact command used.

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  • I tried several times but the table file always is empty. 

    Here is my command 

    gatk HaplotypeCaller -R peach_trinity_v2.fasta -I SRR7589951_mdup.bam -O SRR7589951.vcf
    gatk VariantsToTable -V SRR7589951.vcf -O SRR7589951_table.txt

    Also below is my entire pipeline -- 

    Any help is highly appreciated. 

     

     

    sratoolkit
    fastq-dump SRR7589950 --gzip --split-files
    fastq-dump SRR7589951 --gzip --split-files

    trimmomatic
    TrimmomaticPE -phred33 SRR7589950_1.fastq.gz SRR7589950_2.fastq.gz SRR7589950_1_Q20.fastq.gz SRR7589950_1_unpar.fastq.gz SRR7589950_2_Q20.fastq.gz SRR7589950_2_unpar.fastq.gz LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:30
    TrimmomaticPE -phred33 SRR7589951_1.fastq.gz SRR7589951_2.fastq.gz SRR7589951_1_Q20.fastq.gz SRR7589951_1_unpar.fastq.gz SRR7589951_2_Q20.fastq.gz SRR7589951_2_unpar.fastq.gz LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:30


    trinity
    bowtie2
    jellyfish
    salmon
    Trinity --seqType fq --left SRR7589950_1_Q20.fastq.gz,SRR7589951_1_Q20.fastq.gz --right SRR7589950_2_Q20.fastq.gz,SRR7589951_2_Q20.fastq.gz --max_memory 70G


    transrate
    transrate --assembly peach_trinity.fasta

    ------------------------------------------------------
    bowtie2
    bowtie2-build peach_trinity.fasta bt2_peach
    bowtie2 -x bt2_peach --sensitive-local -q -1 SRR7589950_1_Q20.fastq.gz -2 SRR7589950_2_Q20.fastq.gz | samtools view -Sb -o SRR7589950.bam
    bowtie2 -x bt2_peach --sensitive-local -q -1 SRR7589951_1_Q20.fastq.gz -2 SRR7589951_2_Q20.fastq.gz | samtools view -Sb -o SRR7589951.bam
    ------------------------------------------------------

    gatk

    gatk CreateSequenceDictionary -R peach_trinity_v2.fasta -O peach_trinity_v2.dict
    samtools faidx peach_trinity_v2.fasta

    gatk FixMateInformation -I SRR7589950.bam -O SRR7589950_fixed_mate.bam
    gatk FixMateInformation -I SRR7589951.bam -O SRR7589951_fixed_mate.bam

    gatk AddOrReplaceReadGroups -I SRR7589950_fixed_mate.bam -O SRR7589950_fixed_mate_gr.bam --RGID E00516.1 --RGLB libSRR50 --RGPL ILLUMINA --RGPU HCNJ5ALXX --RGSM peachYL
    gatk AddOrReplaceReadGroups -I SRR7589951_fixed_mate.bam -O SRR7589951_fixed_mate_gr.bam --RGID111111 E00516.5 --RGLB libSRR51 --RGPL ILLUMINA --RGPU HCNJ5ALXX --RGSM peachHJ

    samtools sort -T SRR50-temp -o SRR7589950_sorted.bam SRR7589950_fixed_mate_gr.bam
    samtools sort -T SRR51-temp -o SRR7589951_sorted.bam SRR7589951_fixed_mate_gr.bam

    gatk ValidateSamFile -I SRR7589950_sorted.bam -MODE SUMMARY -R peach_trinity_v2.fasta
    gatk ValidateSamFile -I SRR7589951_sorted.bam -MODE SUMMARY -R peach_trinity_v2.fasta

    gatk MarkDuplicates -I SRR7589950_sorted.bam -O SRR7589950_mdup.bam -M SRR50_mdup_metrics.txt
    gatk MarkDuplicates -I SRR7589951_sorted.bam -O SRR7589951_mdup.bam -M SRR51_mdup_metrics.txt


    gatk ValidateSamFile -I SRR7589950_mdup.bam -MODE SUMMARY -R peach_trinity_v2.fasta
    gatk ValidateSamFile -I SRR7589951_mdup.bam -MODE SUMMARY -R peach_trinity_v2.fasta

    samtools index SRR7589950_mdup.bam
    samtools index SRR7589951_mdup.bam

    gatk HaplotypeCaller -R peach_trinity_v2.fasta -I SRR7589950_mdup.bam -O SRR7589950.vcf

    gatk HaplotypeCaller -R peach_trinity_v2.fasta -I SRR7589951_mdup.bam -O SRR7589951.vcf

     

     

     

     

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  • Avatar
    Bhanu Gandham

     

    1. By default, the tool only extracts PASS or . (unfiltered) variants in the VCF file. Filtered variants may be included in the output by adding the --show-filtered flag. Take a look at the tool doc: https://gatk.broadinstitute.org/hc/en-us/articles/360036711531-VariantsToTable
    2. You also need to provide the INFO (i.e. site-level) fields or FORMAT (i.e. sample-level) fields you want to see in the table with the VariantsToTable command.
    3. If the above suggestions don't work please post the new command here with the output log.
    4. Can you please confirm that the vcf file generated has variant records in it? Please post a few variant records from the vcf file.
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