Hi All,
Is there any reason why the order in which .bam files are given to mpileup would affect the number of sites in the mpileup file?...
24 results in 0.0030 seconds.
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mpileup and multiple input files
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SNP at every chromosome position
Hi,
I SOLiD sequencing data. After aligning with SHRiMP2, I used samtools mpileup for SNP calling:
samtools mpileup -C50... -
Why is samtools mpileup reporting all zero quality scores?
Hi everyone.
I'm calling some variants using samtools from a BWA-aligned and sorted BAM.
For some reason, the samtools mpileup... -
samtools mpileup not filtering reads that fail mapping/base quality filters
Hi all,
I was wondering if anyone could help me with this issue. I am trying to create VCF files using samtools mpileup and would like... -
samtools mpileup -L argument
Argument -L in samtools mpileup "skips INDEL calling if the average per-sample depth is above INT [250]". Why do we need this option? Why INDELs... -
how does samtools mpileup handle the md tag
Hello everyone,
How does samtool mpileup handle the md tag?
I want to know this because the samtools calmd program takes over the... -
Samtools mpileup finds SNPs on each position
Hello everyone,
I am trying to use samtools mpileup. I am using the settings:
...Code:samtools mpileup -f ../chr12Ref.fa chr12.bam >
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How to convert complete bam to mpileup
Hey,
While doing mpileup, I could see that lot of reads are not counted in mpileup output although I could see them in tview,
I am using... -
Samtools mpileup - start and end segments
Hi,
I'm having a problem calling a variant with NGS which has been confirmed via Sanger sequencing.
I'm using samtools mpileup... -
Where is the denovogear output?
Dear all,
I am trying to use DeNovoGear for DNM in trios and have used mpileup using the following command
samtools mpileup -gDf hg19.fasta... -
Problems when calling SNPs using samtools mpileup
Hi there,
Recently, I'm using samtools mpileup to call SNPs using low coverage (average 1x) resequencing data of 600+ populations. But I encountered... -
Samtools consensus sequence error
Dear All
I am again posting this question to the Bioinformatics forum as I didn't get the answer from the Illumina forum.
... -
Speeding up .sam to .vcf creation
I'm trying to get .vcf files from a .sam file via the following commands:
...Code:samtools view -bt ${fai} ${prefix}.sam > ${prefix}_unsorted.bam -
Aligned position within a read from Samtools mpileup
Hello,
Is it possible to infer the aligned position within a read (1-101) of every read in the alignment from a mpileup file?
... -
vcfutils.pl varFilter removes INDELs even with default override
Dear All,
I am running vcfutils.pl varFilter and I have deliberately set all options to very low values to override the defaults so no...
