Question: Converting a CLC variant pipeline to Galaxy
1
gravatar for Mic
2.3 years ago by
Mic70
Australia
Mic70 wrote:

Hello,
I have a recieved a VCF file wich was generated by CLC. Currently, I try convert the below CLC steps to Galaxy. I tried to use vcfannotate and VCF-VCFintersect, but I do not get the same results.
 
    1. Annotate with Overlap Information using parameters:
         * Overlap track = TruSight_One_v1.1_Blood_Group_Genes_BED
     2. Filter based on Overlap using parameters
         * Overlap track = TruSight_One_v1.1_Blood_Group_Genes_BED

        * Keep overlapping = Keep annotations that overlap
     3. Annotate with Overlap Information using parameters:
         * Known variants track = snp142Common
         * Automatically join adjacent MNVs and SNVs
     4. Filter against Known Variants using parameters:
         * Known variants track = snp142Common
         * Join adjacent MNVs and SNVs = No
         * Filter action = Keep variants with overlap found in the track of known variants
     5. Functional Consequences ? Amino Acid Changes using parameters:
         * CDS track = genome (CDS)
         * Sequence track = genome (Genome)
         * mRNA track = genome (mRNA)
         * Filter synonymous variants = Yes
         * Genetic code = 1 Standard
         * Filter CDS regions with no variants = Yes

Does anyone know how to convert the above CLC steps to Galaxy?

Thank you in advance.

Mic

snpeff bed variant annotation vcf • 649 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Mic70
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