RefFinder

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

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