Thank you, Tom. I tried both your suggestions, but the result is the same. I'll try to move all the input files to the same directory, to see if it makes the difference for some reason. In the mean while, do you think I am using the right approach to achieve my purpose - i.e. getting the coverage of each individual allele-?
Thanks, Max ________________________________________ From: Thomas W. Blackwell [[email protected]] Sent: Tuesday, September 09, 2014 9:06 AM To: Tagliamonte,Massimiliano S Cc: [email protected] Subject: Re: [Samtools-help] Intrasamle diversity and allele support 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 > ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
