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