FastCall - PlantGeneticsLab/TIGER GitHub Wiki
Superfast variant calling and genotyping for whole-genome shotgun (WGS) sequencing data. It works for species with disomic inheritance, e.g. diploid species or allopolyploid species, including both inbreds and outcrossers.
Java 8
http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
Samtools
http://samtools.sourceforge.net/
The options of FastCall are listed below.
-app App name.
-a Reference genome file with an index file (.fai). The reference should be in Fasta format. Chromosomes are labelled as numbers (1,2,3,4,5...).
-b Taxa bam information file, including the info about what bams are included for each taxon. The template of the file is available from here.
-c Combined error rate from sequencing and alignment. When the error rate is low, heterogeneous sites are more likely to be called as heterozygous, and vice versa. It is 0.05 by default.
-d Individual depth ratio. This is the depth of the lower-depth allele vs. total depth. When the threshold is low, heterogeneous sites are more likely to be called as heterozygous, and vice versa. It is 0.4 by default.
-e P-value threshold of Mendelian segregation test. Lower threshold (e.g. 1, the test will be removed) is recommended if rare alleles are the major interest. It is 1 by default.
-f Minor allele occurrence threshold, representing the minimum number of taxa where the minor allele exist. It is 2 by default.
-g Chromosome or region on which genotyping will be performed (e.g. chromosome 1 is designated as 1. Region 1bp to 100000bp on chromosome 1 is 1:1,100000).
-h VCF output directory.
-i Number of threads for pileup.
-j The path of samtools.
Here is an example of running FastCall from command line,
- java -Xmx100g -jar TIGER.jar -app FastCall -a chr001.fa -b taxaBamMap.txt -c 30 -d 20 -e 2 -f 0.2 -g 3 -h 0.8 -i 0.4 -j 0.2 -k 1 -l 32 -m /ing -n /usr/local/bin/samtools > log.txt &
Fei Lu
[email protected]; [email protected]