From Genome Analysis Wiki
Jump to navigationJump to search
459 bytes added
, 18:38, 2 February 2012
Line 61: |
Line 61: |
| arf -a complexity 1000g.vcf -g genome.fa -l 30 | | arf -a complexity 1000g.vcf -g genome.fa -l 30 |
| | | |
− | == In development == | + | == In development/Pending update == |
| | | |
| #annotates variants | | #annotates variants |
− | ##INFO=<ID=,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR"> | + | ##INFO=<ID=VTYPE,Number=1,Type=string,Description="Annotates variant by types SNP, MNP, INDEL, SV, CR"> |
| #-l option defines the length in which to differentiate INDELs and SVs | | #-l option defines the length in which to differentiate INDELs and SVs |
| arf -a vartype 1000g.vcf -l 30 | | arf -a vartype 1000g.vcf -l 30 |
| + | |
| + | #compute [[Genotype Likelihood Based Allele Balance]] |
| + | ##INFO=<ID=AB,Number=1,Type=float,Description="Allele Balance computed from genotype likelihoods"> |
| + | #requires PL/GL and DP in the genotype fields |
| + | arf -a ab 1000g.vcf |
| + | |
| + | #-e option |
| + | #when used in conjunction with an analysis that requires allele or genotype frequency estimates, |
| + | #will attempt to find estimates in the AF, GF and HWEAF fields |
| + | arf -a ab 1000g.vcf -e |
| | | |
| == Command Line Options == | | == Command Line Options == |
Line 98: |
Line 108: |
| You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from the fasta file named human.g1k.v37-bs.umfa. | | You will also need a copy of human genome assembly fasta file: [http://www-personal.umich.edu/~atks/human.g1k.v37.fa.gz human.g1k.v37.fa]. Please gunzip it before usage. arf will generate a memory mapped file from the fasta file named human.g1k.v37-bs.umfa. |
| | | |
− | You will also need a copy of UCSC refGene text file: [http://www-personal.umich.edu/~atks/refGene.txt.gz refGene.txt.gz]. | + | You will also need a copy of UCSC refGene text file: [http://www-personal.umich.edu/~atks/refGene.txt.gz refGene.txt]. |
| | | |
| | | |
| This page is maintained by [mailto:atks@umich.edu Adrian]. | | This page is maintained by [mailto:atks@umich.edu Adrian]. |