Pre-Alignment process

Question

[AIMAR]

Good morning everyone, Hope yall doing well I would like to ask here where can I dowload the dbSNP et Mills_and_1000G_gold_standard.indels for as reference genome GRCh 37 GCF_000001405.13

I need them for my genomic variant analysis and also, is there any ressources concerning how to perform the READ DEPTH MEASURE for the post-alignment part..?

Answer 1

[GenoMax]

You will find the gold standard indels file by doing

$ wget ftp://[e-mail]/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

Is this what you are looking for read depth: https://gatk.broadinstitute.org/hc/en-us/articles/360035532112-Coverage-Read-depth-metrics