RefFinder: Difference between revisions

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cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst
cmp tst small.bam
cmp tst small.bam
</pre>
possible options are
;inputIsZero
;full
These are flags, so examples are
<pre>
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
</pre>
Or if we want the chr position also
<pre>
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
</pre>
Or if the positions are zero index as opposed to one indexed:
<pre>
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
</pre>
</pre>

Revision as of 16:00, 12 March 2014

Small fast cprogram to extract bases from a fasta file.

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