Pre-Alignment process
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..?
1 answer
You will find the gold standard indels file by doing
$ wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/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
Log in to answer this question.
More posts like this
-
Variant calling RADseq and WGS population genomic datasets
written by Stephen •
-
Refflat file for Rattus norvegicus
written by AIMAR •
-
About FastP Tool
written by AIMAR •
-
How to check normal BAM_files before create a Panel Of Normals (PoN)
written by AIMAR •
-
BQSR using GATK BaseRecalibrator
written by Fatemeh Nabizadeh •
-
From which genome assembly do these coordinates come?
written by Basti •
-
News: New NCBI Datasets home and documentation pages provide easier access
written by e.cox •
-
dbSNP annotation database and appropriate filtering in somatic variant calling pipelines
written by svlachavas
-
What is the name of this build What is equivalent to build37.fa.bz2
written by Daisy •
-
preprocessing genome fasta file prior to mapping?
written by lstbl •
