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Why I couldn't download vcf files from public FTP servern any more?

Lisa0508Lisa0508 Ann Arbor, MIMember

Dear GATK team,
I got my raw variant vcf output. Now I want to perform VQSR with those raw variants. Some VCF files in the resource bundle need to be downloaded for variant recalibration. I don't know why I can't access to the resource today. When I click into the "our public FTP server" link. Nothing showed up. It's quite weird because I just downloaded some dbSNP VCF files yesterday without even log-in. It didn't ask me for Username and Password. Sorry about the trouble. Looking forward to your reply.

Best Answers

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We're currently experiencing some technical difficulties and hope to have the FTP back to normal working order very soon. Sorry for the inconvenience.

  • Lisa0508Lisa0508 Ann Arbor, MIMember

    Thank you very much for your answer! I have tried the password at that thread. It was not correct though.
    May I ask you another question?
    You recommended to use both "Mills_and_1000G_gold_standard.indels.b37.sites.vcf and 1000G_phase1.indels.b37.vcf" for RealignerTargetCreator or IndelRealigner. Is it possible to include both site at one run? I found if I wrote the command as follows trying to include two known sites at once. It would report error. So I used only the "Mills_and_1000G_gold_standard.indels.hg19.sites.vcf" for -known option.Was it enough just using one data set for calibration then? Thank you again

    java -Xmx4g -jar $GATK_JARS/GenomeAnalysisTK.jar \
    -T IndelRealigner \
    -R /home2/Human_genome_reference/ucsc.hg19.fasta \
    -I /home2/test_07242015/Dedup_aligned_TKDNFE_012_ver2.sorted.bam \
    -targetIntervals /home2/test_07242015/target_interval_Dedup_aligned_TKDNFE_012.list \
    -known /home2/zhanghon/Human_genome_reference/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
    -known /home2/Human_genome_reference/1000G_phase1.indels.b37.vcf \
    -o Realigned_dedup_aligned_TKDNFE_012_ver2.sorted.bam

    Have a nice day,
    :smile: Lisa

  • Lisa0508Lisa0508 Ann Arbor, MIMember

    Thank you very much! The command line worked well.

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