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
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
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