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