Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites

Dear James, I have installed the latest github htslib, samtools and bcftools Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) Version: 1.5-13-gab7b4c1 (using htslib 1.5-5-gda5c0c7) and still I get not the full number of sites. However, it seems that these are all

Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites

On Wed, Jul 12, 2017 at 05:54:06PM +0200, Kristian Ullrich wrote: > HOWEVER, if I add the options '-u -v' so that the output should be > uncompressed and in VCF format, than the output has duplicated > POSITIONs and in total less than the expected 25000 sites, if I > remove the duplicated. So

Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites

On Wed, Jul 12, 2017 at 04:41:17PM +0200, Kristian Ullrich wrote: > whatever I am doing with both 'samtools mpileup' and 'bcftools > mpileup', in both cases not all sites are reported, even if I > specify the '-a -a' options e.g.: My standard first try at explaining anything odd with mpileup is

[Samtools-help] samtools mpileup / bcftools mpileup / missing sites

Dear samtools-help list, whatever I am doing with both 'samtools mpileup' and 'bcftools mpileup', in both cases not all sites are reported, even if I specify the '-a -a' options e.g.: samtools mpileup -L 9 -d 9 -r chr1:5001-50025000 -b BAM.list --fasta-ref REF.fasta -a

[Samtools-help] samtools mpileup help

Hi Admin, I run samtools mpileup using the following parameters. samtools mpileup -B -q 1 -f $ref -l $bedFile $3/$4_Tumor.sorted.bam > $3/$4_Tumor.pileup I found that the pileup file also the eventual vcf has variants in positions not in the bed file. There are around 30 such variants out of

Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta

John -- Thank you for your quick response. The commands -t and --skip-indels were used because I was originally outputting to vcd, but I subsequently verified that the problem was at the level of mpileup output. Yes, working with human -- hg19. I will check on the two things that you mention, but

Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta

On 14 Dec 2016, at 11:54, John Marshall wrote: > > On 13 Dec 2016, at 23:56, Jacob Ulirsch wrote: >> Here is output from faidx, showing the correct fasta sequence for these >> positions: >> >> samtools faidx mtDNA.fasta chrM:1330-1340 >>>

Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta

On 13 Dec 2016, at 23:56, Jacob Ulirsch wrote: > When I run samtools (v1.3.1) mpileup I am running into some very concerning > issues. The reference bases for the output pileup file are not in the same > position as the references in the input fasta. In fact, they

[Samtools-help] Samtools mpileup reference is different from input reference fasta

Hello, When I run samtools (v1.3.1) mpileup I am running into some very concerning issues. The reference bases for the output pileup file are not in the same position as the references in the input fasta. In fact, they appear to be oddly shifted. For example, here is output for 10 variants from

Re: [Samtools-help] samtools mpileup

Hi, On Mon, Sep 19, 2016 at 05:32:44PM +0800, peijia wrote: > I use samtools with the version 1.3.1 to execute the command "samtools > mpileup -uf REF.fasta merge.bam -o merge.bcf", the result shows "[mpileup] 1 > samples in 1 input files Set max per-file depth to 8000" and it > doesn't work.

[Samtools-help] samtools mpileup

Does mpileup support multi-nucleotide substitutions, e.g. a dinucleotide substitution ? The version I have, treats them as two separate independent single substitutions even when all variant reads have both the substitutions. If it not available currently, is it something that samtools plans to

Re: [Samtools-help] samtools mpileup genotype likelihood calulation

What is the coverage of your bams? samtools samples randomly 255 reads when calculating genotype likelihoods. petr On Mon, 2016-02-01 at 09:35 -0500, Thomas W. Blackwell wrote: > See option -d, --max-depth. Also -F, -L, -m for indel calling. > > These count all reads overlapping a candidate

Re: [Samtools-help] samtools mpileup genotype likelihood calulation

Hi Gunter, this is for each a pileup position regardless of the start coordinate. There is an expensive step in the calculation which is solved by keeping a pre-calculating table for number of reads up to 255. This constraint cannot be easily removed, but 255 reads should be plenty for

[Samtools-help] samtools mpileup genotype likelihood calulation

Dear Samtools-Team, I encountered that samtools mpileup followed by bcftools for variant calling produces different results when the bam file is sorted differently. Since the bam file has to be sorted by coordinate, the order of reads sharing the same start position may vary in different

Re: [Samtools-help] Samtools mpileup: some positions missing fields

On 16 Sep 2015, at 22:24, Brendan Kohrn wrote: > I found the following issue in the output from samtools mpileup (-f), with a > single bam file input: > > gi|255961284|ref|NC_011713.2| 140 G 1 ,$ C > gi|255961284|ref|NC_011713.2| 149 A 0 >

Re: [Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities)

—ignore-overlaps option was what was needed to get the pre-v1 mpileup output. Thanks. Petr. On Feb 2, 2015, at 12:50 AM, Petr Danecek p...@sanger.ac.uk wrote: Hi Paul, I think this might be related to bug fixes where the default MQ and BQ filters were not applied with the raw

Re: [Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities)

Hi Paul, I think this might be related to bug fixes where the default MQ and BQ filters were not applied with the raw mpileup output. Petr On Fri, 2015-01-30 at 15:07 -0800, Paul Lott wrote: Hi all, We have an amplicon pipeline that uses mpileup output. We recently updated samtools from

[Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities)

Hi all, We have an amplicon pipeline that uses mpileup output. We recently updated samtools from 0.1.19 to 1.1. When performing some validation on the pipeline, we found that there were a significant number of variants missing from the caller(Varscan 2.3.7) output. The only difference was

[Samtools-help] samtools mpileup -- error status 141

Hello, I observe a strange problem and I am not able to find out what is the exact reason of it. When I use samtools mpileup | another_program, samtools return error code 141. Everything else is OK (pileup is well created, all data are well processed). I observe it when I use set -o pipefail. The

Re: [Samtools-help] samtools mpileup -- error status 141

On 13 Nov 2014, at 12:23, Karel Břinda karel.bri...@gmail.com wrote: I observe a strange problem and I am not able to find out what is the exact reason of it. When I use samtools mpileup | another_program, samtools return error code 141. When a Unix shell reports that a command has an exit

Re: [Samtools-help] samtools mpileup -- error status 141

Hello, thanks a lot for this excellent answer. Thanks to it I found where originally the problem started. So as I realized, it appeared only with FASTA files containing space in the first line (i.e., with a sequence description). The program mentioned in my previous e-mail as another_program

[Samtools-help] samtools mpileup call snp

hi all ; I call snp by samtools mpileup and get results of vcf format; and i find the quality of snp which most are 222,and the max of them are also 222, could you tell me the reasons. I am looking foward to hearing from you soon. Sincerely,