Code:
/usr/local/sw/bcftools-1.9/bcftools mpileup -f /mnt/NEOGENE2/share/ref/genomes/hsa/hs37d5.fa
87 results in 0.0036 seconds.
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Bcftools Mpileup bias for alternative alleles?
I have called snps from a bam file using the below commands:
... -
SNP calling using samtools
Hi all,
I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand... -
confusion about BCFtools "EXPRESSIONS" flags
I'm hoping someone can help me understand the "EXPRESSIONS" flags used in bfctools.
I'm trying to filter variants from a vcf... -
mpileup core dumped error with input fasta aligned bamfile.
I did bwa mem human alignment with single end fasta file. I tried running samtools mpileup & i'm getting same error as mentioned in thread as :Aborted... -
Samtools mpileup: Discrepancies in indel coverage
In .vcf files outputted by samtools the coverage of indels is represented by the IDV(Maximum number of reads supporting an indel) value. This value corresponds... -
mpileup sample specific read count/quality info
Hello,
I am looking to use mpileup for base calling. Previously I ran samples together but could not find any sample specific read count/quality... -
mpileup to STRUCTURE
Hi all,
Thought I would see if anyone has a different (better!) pipeline for collecting a set of SNPs from many bam files for use with STRUCTURE... -
samtools mpileup possible bug
Hello,
I noticed that last sample (last 3 columns) in mpileup format behave strangely in positions with low base quality (< 13). It looks... -
samtools mpileup segfault with positions list
Hello,
I am using samtools v 1.2 on a machine with Ubuntu 14.04.2 and I am trying
to generate a SNP table from sorted bam files... -
bcftools issue
Folks:
I have a mouse sequencing project with multiple .bam files generated.
samtools version 0.1.19-44428cd
bcftools... -
Samtools MPILEUP on single-end/paired-end data
Hi everybody,
for variant calling, i am using samtools mpileup.
as far as i know, mpileup is by default ignoring certain... -
error when running samtools mpileup and bcftools
Hi all
I run the code below which is modified from [1]
samtools mpileup -uf wg.fa ERR000589.srt.bam | /home/linp/linpDisk4/DataSeq/bcftools/bcftools... -
Looking at specific positions in a BAM file for SNPs
Hi, I have a bunch of BAM files of mapped RNAseq reads to the human genome.
I also have a list of known positions where SNPs may or may not...Last edited by danwiththeplan; 04-29-2014, 02:10 PM. -
samtools mpileup multiple bam files
Hi,
I am trying to run samtools mpileup on multiple bam files but for some reason I am getting the error "view: invalid option -- 'b'"...Last edited by lizzi; 04-08-2014, 03:59 AM. -
varscan2 mpileup2snp output differs from mpileup output
I have a problem understanding the output of VarScan mpileup2snp.
I use samtools mpileup to generate the pileup (samtools 0.1.18).
...
