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