RefFinder: Difference between revisions
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Small fast cprogram to extract bases from a fasta file. Download here [http://popgen.dk/software/download/refFinder/refFinder.tar.gz] | Small fast cprogram to extract bases from a fasta file. Download here [http://popgen.dk/software/download/refFinder/refFinder.tar.gz] | ||
Program can either work as a standalone program, or allow for easy retrieval of reference bases by using the API. | |||
=Install= | =Install= | ||
<pre> | <pre> | ||
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</pre> | </pre> | ||
=Example= | =Stand alone= | ||
==Example== | |||
Generate samtools chr pos ref doing | Generate samtools chr pos ref doing | ||
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1 13999911 g | 1 13999911 g | ||
</pre> | </pre> | ||
=API= |
Revision as of 12:42, 13 March 2014
Small fast cprogram to extract bases from a fasta file. Download here [1]
Program can either work as a standalone program, or allow for easy retrieval of reference bases by using the API.
Install
wget http://popgen.dk/software/download/refFinder/refFinder.tar.gz cd refFinder/ make cd ..
Stand alone
Example
Generate samtools chr pos ref doing
samtools mpileup -b smallBam.filelist -f /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa |cut -f1-3 >small.sam
Use refFinder to find the bases for each position in small.sam
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst cmp tst small.bam
possible options are
- inputIsZero
- full
These are flags, so examples are
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa |head a g c t a c t c g g
Or if we want the chr position also
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full |head 1 13999902 a 1 13999903 g 1 13999904 c 1 13999905 t 1 13999906 a 1 13999907 c 1 13999908 t 1 13999909 c 1 13999910 g 1 13999911 g
Or if the positions are zero index as opposed to one indexed:
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full inputIsZero |head 1 13999902 g 1 13999903 c 1 13999904 t 1 13999905 a 1 13999906 c 1 13999907 t 1 13999908 c 1 13999909 g 1 13999910 g 1 13999911 g