Max -
At a guess, the difficulty is from putting the output file last
on the command line. Traditionally, the region specifier has to
be the last field on the command line (and you can add as many
different region specifiers, space separated, as the command line
buffer will allow. Please try putting '-o alignment.test'
immediately after '-h' for example, or else immediately after
'-t reference.fasta.fai'.
- tom blackwell -
On Tue, 9 Sep 2014, Tagliamonte,Massimiliano S wrote:
> 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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