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Rami Kheireddine

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Latest activity by Rami Kheireddine
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    Rami Kheireddine created a post,

    Annotation for variant calling

    1. Community
    2. General Discussion

    REQUIRED for all errors and issues: a) GATK version used: 4.4.0.0b) Exact command used: gatk-4.4.0.0/gatk VariantAnnotator     -R /home/databench/GRCz11_RefData/GRCz11.fa     -A SnpEff     --varian...

    • Rami Kheireddine
    • 2 followers
    • 1 comment
    • 1 vote
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    Rami Kheireddine commented,

    1. Community
    2. Non-Human
    3. Annotate using funcotator

    Do you know what the format of the file should be? 

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    Rami Kheireddine created a post,

    Annotate using funcotator

    1. Community
    2. Non-Human

    I am trying to use : ./gatk Funcotator \     --variant variants.vcf \     --reference Homo_sapiens_assembly19.fasta \     --ref-version hg19 \     --data-sources-path funcotator_dataSources.v1.2.20...

    • Rami Kheireddine
    • 4 followers
    • 6 comments
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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    Hello Skywarrior! Just wanted to let you know the run is finally over (took 28hrs). Thank you so much for your response, I really appreciate it.

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    The current locus is 3 in 238 minutes. I assume there are 26 thousand loci in Zebra Fish. So, I guess I have a long wait! :(   

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    Is there a way to tell how long it will take to be done, or when it is close to the end?  

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    Yes this is a virtual machine. I managed to increase the number of threads on it. And it is currently moving 3 times faster. Will this run take a long time to finish?  

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

     gatk-4.4.0.0/gatk HaplotypeCaller -R /home/databench/GRCz11_RefData/GRCz11.fa -I Routput_sorted_dedup_bqsr_reads.bam -O Routput_raw_variants.vcf Using GATK jar /home/databench/gatk-4.4.0.0/gatk-pa...

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    The log is very long (went on for 6 days). I stopped it at the end. Yes my system support AVX. Can you help me split the intervals into separate instances? 

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    Rami Kheireddine commented,

    1. Community
    2. Other
    3. Haplotype caller taking too long

    The code ran for 7 days and it did not finish. Any suggestions on how to make it go faster ?