Atlas-SNP

Atlas-SNP

Atlas-SNP2 is designed to evaluate and distinguish true SNP from sequencing and mapping errors in whole-exome capture sequencing (WECS) data.

For 454/Illumina data

ruby Atlas-SNP2.rb Atlas-SNP2.rb -i [in.sorted.bam] -r [reference.fa] -o [output file] -n [sample name] [choosing platform]

Atlas-SNP2 is coded in Ruby and basic usage can be viewed by running the program without any argument.
-i FILE BAM format alignment file (Required to be sorted by start position)
-r FILE FASTA format reference sequence file (Required)
-o STR name of output result file (Required)
-n Sample name used in VCF file (Required)
-t STR Only call SNP on given target region (Optional, please refer "samtools view" for the target region format)
-a FILE file contaning sites will always be included(optional)
-F Include filtered lines in the output that have a QUAL of at least 1

Choosing Platform (Default is 454 FLX)
-s Illumina
-x 454 Titanium

Setting up prior probability
-e FLT Prior(error|c) when variant coverage number is above 2 for 454 and Illumina data (Default is 0.1)
-l FLT Prior(error|c) when variant coverage number is 1 or 2 for 454 data (Default is 0.9)

Setting up filters
-c Posterior probability cutoff (Default is 0.95)
-y Minimal Coverage required for high confidence SNP calls (Default is 8)
-m FLT maximum percentage of substitution bases allowed in the alignment (Default is 5.0)
-g FLT maximum percentage of insertion and deletion bases allowed in the alignment (Default is 5.0)
-f INT maximum number of alignments allowed to be piled up on a site (Default is 1024)
-p INT insertion size for pair-end re-sequencing data (Default is 0)

Example
# Call SNP of one Illumina BAM only on chr1 and output the SNP results in VCF file ~/NA12275.chr1.snp.vcf

ruby Atlas-SNP2.rb -i NA12275.bam -r ~/refs/human_g1k_v37.fasta -o NA12275.chr1.snp –s –t chr1 –v –n NA12275

For SOLiD data

SOLiD-SNP-caller \<in.bam> \<ref.fa> [.bed region] > [output.vcf]

SOLiD-SNP-caller is coded in C++ and basic usage can be viewed by running the program without any argument.
\<in.bam> FILE BAM format alignment file (Required to be sorted by start position)
\<ref.fa> FILE FASTA format reference sequence file (Required)
\<.bed> FILE Only call SNP on given regions defined in bed format (optional)

Example
# Call SNP of one SOLiD BAM only on coding regions and output the SNP results in VCF file NA20532.ontarget.vcf

SOLiD-SNP-caller NA20532.bam ~/refs/human_g1k_v37.fasta ccds.bed > NA20532.ontarget.vcf

For Ion Torrent data

Analysis capabilities for the Ion Torrent PGM are currently in the late stages of development.

There will be an announcement once Atlas2 is updated to incorporate Ion Torrent analysis into the Suite. Comprehensive documentation will also be added to this wiki page at that time.