Hi dear community,
I don't have any experience in variant calling, and I have to solve this problem:
Using the most recent VCF file describing ClinVar variants and a bed/gff file of the coding sequence of curated RefSeq genes, write a script that outputs all the pathogenic and likely pathogenic variants that are found inside genes and have coverage less than 10x in the BAM file. the script should output a table with each ClinVar variant’s chromosome, genomic position, reference and alternate alleles, coverage in the BAM file and all the RefSeq transcripts that are affected by the variant.
I have an access to a basespace project which contains analysis (vcf, bam...) of some biosamples (s01-NFE-CEX-NA12878-demo...)
And I really don't know how to start to solve this problem
I will glad to get some help
Thank you very much