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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]
=Install=
<pre>
</pre>


=Example=
=Example=

Revision as of 16:04, 12 March 2014

Small fast cprogram to extract bases from a fasta file. Download here [1]

Install


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