error message with samtools converting pileup to vcf

[kym]

Hi,

I am new to sequencing. I use samtools 0.1.15 to run the pile up

samtools pileup -vcf hg19.fasta sample_removed_duplicates_sorted.bam > sample_pileup.pre
$SAMDIR/misc/samtools.pl varFilter -d 15 -S 30 -i 30 -Q 50 -q 50 sample_pileup.pre| awk '$6>=20' > sample_pileup

and then call snps with

$SAMDIR/misc/sam2vcf.pl -r hg19.fasta -R -s < sample_pileup
> sample_pileup.snps.vcf

This all went fine.
I use
$SAMDIR/misc/sam2vcf.pl -r reference.fasta -R -i < sample_pileup
> sample_pileup.indels.vcf

Error message:
Can't exec "samtools": No such file or directory at /home/samtools-0.1.15/misc/sam2vcf.pl line 238, <STDIN> line 7.
samtools faidx hg19.fasta chr1:1289367-11289367: No such file or directory at /home/samtools-0.1.15/misc/sam2vcf.pl line 151

I have already index the hg19.fasta with samtools faidx and put in the same directory as the hg19.fasta

Thanks very much for comments

[TsviyaOlender]

Hi,
I am also a new user and experiencing the same problem.
Did you solve it by now>

Thanks