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Question: hgvs_vcf input format?
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gravatar for galaxyNewbie
3 months ago by
galaxyNewbie • 30
galaxyNewbie • 30 wrote:

For the HGVS_VCF package it appears the input format is simply a tabular file. I uploaded a .txt file with validated HGVS formatted entries. Could anyone provide information about the input formatting to the HGVS_VCF galaxy package?

Are there any galaxy package alternatives which would convert hgvs formats into a vcf file?

Thank you!

galaxy hgvs vcf • 163 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by galaxyNewbie • 30
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I've not used this tool but found the underlying code that describes the input column ordering. To make sure the values for the columns are valid for HGVS format, review the file specification at https://varnomen.hgvs.org/.

For use in Galaxy, you may need to assign the datatype tabular to the input dataset if you haven't done that already. I can't determine if txt or tabular is required by the tool (or maybe both are accepted). You'll need to test that out. https://galaxyproject.org/support/metadata/

Details:

Each $ variable represents a data column in the order expected.

my ($chr_column, $pos_column, $ref_column, $alt_column, $alt_cnt_column, $tot_cnt_column, $dbid_column, $cdna_hgvs_column, $aa_hgvs_column, $transcript_column, $zygosity_column, $caveats_column, $phase_column, $pvalue_column, $genename_column);

Another part of the code that labels the $ variables.

    "Chr" => \$chr_column,
    "DNA From" => \$pos_column,
    "Gene Name" => \$genename_column,
    "Ref base" => \$ref_column,
    "Obs base" => \$alt_column,
    "Variant Reads" => \$alt_cnt_column,
    "Total Reads" => \$tot_cnt_column,
    "Variant DB ID" => \$dbid_column,
    "Transcript HGVS" => \$cdna_hgvs_column,
    "Protein HGVS" => \$aa_hgvs_column,
    "Selected transcript" => \$transcript_column,
    "Zygosity" => \$zygosity_column,
    "Caveats" => \$caveats_column,
    "Phase" => \$phase_column,
    "P-value" => \$pvalue_column);

Thanks! Jen, Galaxy team

MTS Reference: https://toolshed.g2.bx.psu.edu/view/yusuf/hgvs_vcf/138d81f259c8
ADD COMMENT • link modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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