Dear Samtools users,
I am currently working with Samtools 0.1.19 and trying to carry out a SNP
analysis on a haploid genome. As I am expecting some intrasample diversity, I
would like to know the reads support for alleles within sample. I have obtained
so far a multisample VCF file, and I would like to know the support for each
allele at heterozygous SNP positions in each sample. I am a bit puzzled how to
do this.
As first step, I have tried to use Samtools view, in order to visualize the
alignment in a single position. My command line is:
samtools view -h -t reference.fasta.fai ../sample_1.bam chr1:40,000-40,020 -o
alignment.test
But I get the error:
random alignment retrieval only works for indexed BAM files.
The file sample_1.bam is indexed though, and the relative .bai file is in the
same directory.
Is there any way I can achieve my purpose by using Samtools? Please let me know
if I need to add more information.
Thanks for you help,
Max
Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology
Mob. no. 352 328 9072
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