SAM tools question

[jsun529]

Hello,
Recently I am trying to use samtools to call variants(snp/indel) from the output of BFAST program:XXX.sam
The scrips that executed are follows:
samtools view -bt ref_list.txt -o aln.bam XXX.sam
samtools sort aln.bam aln.sorted
amtools index aln.sorted.bam
samtools pileup -vcf ref.fa aln.sorted.bam > raw.pileup

samtools.pl varFilter raw.pileup > final.pileup

the data I have have higher coverage, I noticed the samtools.pl has a cap on maximum read depth? The question is
a) the result it returned when using default parameters are not what we expected only the low coverage reads are returned
if I reset the -D it returns me nothing. Just wondering what would be the issues here and how to fix it.
The only additional concern is when I do BFAST I supplies an exon file for specific region of interests. For the sam tool reference is the whole gene(intron included) in fasta format, would this be matter for the final result, thought I doubt?

for another gene even the raw.pileup returns nothing. I am wondering what were the paremeters to be reset if at all possible.

Thanks,

[prisnirath]

Hi there,
Your post seems to be quite old...and assuming that you would have found a solution to your question.. I have a similar problem. Can you please suggest me how did you manipulate the read depth?