3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 (view source)
Revision as of 01:02, 15 June 2014
, 01:02, 15 June 2014→Examining GotCloud SnpCall Input files
# Reference genome FASTA file
# Reference genome FASTA file
#* Contains the reference base for each position of each chromosome
#* Contains the reference base for each position of each chromosome
#** Used to compare bases in sequence reads to the reference positions they mapped to
#** Identify SNPs
#* Additional information on the FASTA format: http://en.wikipedia.org/wiki/FASTA_format
#* Additional information on the FASTA format: http://en.wikipedia.org/wiki/FASTA_format
# VCF (variant call format) files with chromosomes/positions
# VCF (variant call format) files with chromosomes/positions
#* dbsnp - used to skip known variants when recalibrating
#* indel - contains known insertions & deletions to help with filtering
#* hapmap - used for sample contamination/sample swap validation
#* omni - used as likely true positives for SVM filtering
#*
#* hapmap - used as likely true positives for SVM filtering and for generating summary statistics
#* dbsnp - used for generating summary statistics
=== GotCloud Configuration File ===
=== GotCloud Configuration File ===
