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<prev • 157 results • page 1 of 6 • next >
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Read depth calling for X chromsome - script modification
read depth calling samtools mpileup written 11 months ago by mbhargava2003 • 0 • updated 20 days ago by Biostar ♦♦ 20
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2
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99
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samtools mpileup output documentation
samtools mpileup output written 4 weeks ago by bec • 0 • updated 4 weeks ago by James Bonfield • 60
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179
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Calling SNPs with low coverage
vcf low-coverage samtools mpileup snp written 9 weeks ago by devin.porter92 • 0 • updated 8 weeks ago by Brian Bushnell ♦ 12k
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130
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mpileup for PacBio reads
quiver calling pacbio mpileup variants written 9 weeks ago by Biomonika (Noolean) ♦ 2.9k
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128
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1
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Pileup file and order of the individuals
order samtools mpileup written 12 weeks ago by AP • 60
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272
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How can I input a BAM file to the samtools mpileup command without using a text file?
variant calling bam samtools mpileup written 3 months ago by cristian • 50 • updated 3 months ago by genomax ♦ 29k
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emtpy bcf file
alignment samtools mpileup written 4 months ago by Illinu • 80
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3
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408
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Generate Consensus sequence from BAM file
psmc samtools mpileup written 4 months ago by SOHAIL • 80
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5 follow
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Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
variant-calling merge samtools mpileup snp written 4 months ago by Rob • 80
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236
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Bam-readcounts min-base-quality not giving expected output
bam-readcount mpileup written 4 months ago by sheenams • 50 • updated 4 months ago by Chris Miller ♦ 18k
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223
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Why does mpileup tell me the starting and ending base of a read?
samtools mpileup written 4 months ago by Peavil • 10
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317
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why allelic count on forward and reverse strand do not add up to depth in the results of samtools mpileup?
vcf samtools mpileup written 5 months ago by murathong • 90 • updated 4 months ago by Tom_L • 180
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What is mean that mpileup read depth (read count) 0?
samtools mpileup written 5 months ago by Peavil • 10 • updated 5 months ago by Devon Ryan ♦ 68k
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Different output from pileup and mpileup commands VarScan
varscan mpileup written 5 months ago by agata88 • 580
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5 follow
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Sam Tools Pileup Format
format samtools mpileup written 5.2 years ago by Vittorio Fortino • 20 • updated 5 months ago by Biostar ♦♦ 20
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How best to parse samtools mpileup results?
vcf samtools vcftools mpileup written 5 months ago by yarmda • 0 • updated 5 months ago by Pierre Lindenbaum ♦ 95k
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219
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Variant calling - display nucleotides with 0 coverage
vcf samtools bcftools mpileup bcf written 6 months ago by yarmda • 0
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230
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How to output all variant alleles at a given site, regardless of quality
variant snp mpileup written 6 months ago by correlationmatrix • 20 • updated 6 months ago by Brian Bushnell ♦ 12k
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236
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Samtools mpileup - Individual Pile-ups vs Group Pile-ups
samtools snp mpileup sequencing written 6 months ago by jrh154 • 0
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1
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337
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1
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varscan misses alternate variant alleles
variant freebayes insertion mpileup deletion written 7 months ago by mark.rose • 10
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277
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1
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MPile up Result contains "X" in Alt column
galaxy samtools mpileup written 8 months ago by Bioinformatician_in_trouble • 10
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Difference between samtools DEPTH and MPILEUP
reads samtools chip-seq mpileup depth written 8 months ago by ariel.balter • 100 • updated 8 months ago by Devon Ryan ♦ 68k
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Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
samtools pysam mpileup written 8 months ago by abascalfederico • 930
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9 follow
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Extract Base Based On Position From Bam File
samtools mpileup written 5.0 years ago by Empyrean • 150 • updated 8 months ago by stephanieP • 0
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1
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399
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Assign missing genotype (./. or N/N) for a SNP in vcf file if DP=0
vcf variant snp mpileup written 8 months ago by berge2015 • 70
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Meaning Of The Initial Column Of Filtered Out By Vcfutils.Pl Varfilter -P
samtools mpileup written 4.6 years ago by bioinformatica2005 • 0 • updated 8 months ago by Biostar ♦♦ 20
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524
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samtools mpileup not calling small (6 base) INSERT
indel vcf samtools mpileup prokaryote written 12 months ago by ALchEmiXt • 1.8k • updated 9 months ago by sb1 • 0
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409
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Running samtools mpileup on BAM that contains colorspace
reference-based bam samtools colorspace mpileup written 10 months ago by Michael Gruenstaeudl • 10
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Error in running a Samtools mpileup script for getting base frequency information
genome mpileup written 10 months ago by jigarnt • 30 • updated 10 months ago by Devon Ryan ♦ 68k
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How to use "Mpileup" for getting information of the reads of the SNP from the BAM files?
genome bam snp mpileup written 10 months ago by jigarnt • 30 • updated 10 months ago by agata88 • 580
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