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<prev • 186 results • page 1 of 7 • next >
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How to read an mpileup file from Samtools into Python
python next-gen samtools mpileup written 25 days ago by M.O.L.S • 0
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Using samtools to assess the number of reads that cover a variant position, as well as the ratio of ref/alt among those reads
allele balance bam samtools rna-seq mpileup written 20 days ago by claudiadast • 0
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How to read my Samtools mpileup?
samtools student mpileup written 4 weeks ago by c.clarido • 40 • updated 4 weeks ago by finswimmer ♦ 6.8k
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Samtools mpileup genotype likelihood no PL field when all individuals are 0/0
pl samtools mpileup written 5 weeks ago by cetin.m • 0 • updated 5 weeks ago by Santosh Anand • 4.0k
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bcftools mpileup output format
bcftools mpileup written 11 weeks ago by tarek.mohamed • 190
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How to add sequence information to vcf from MPileup
vcf bam snp mpileup rna-seq written 11 weeks ago by helge.fluess • 0
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Bcftools view options for SNPs calling.
bcftools samtools snp mpileup written 3.3 years ago by Eddie_I • 20 • updated 3 months ago by Kevin Blighe ♦ 32k
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Order of samtools mpileup - arbitrary or not?
samtools mpileup written 3 months ago by blur • 90 • updated 3 months ago by Devon Ryan ♦ 86k
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Calculate average mapping quality at a position
mapping quality mpileup written 3 months ago by hpapoli • 70 • updated 3 months ago by Gabriel R. • 2.5k
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samtools mpileup `error uninitialized value $l in numeric lt` during BAM to FASTA conversion
fasta samtolls mpileup bam written 4 months ago by marongiu.luigi • 330
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7 follow
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Samtools mpileup degenerative characters
samtools degenrative characters mpileup written 16 months ago by bruseq • 20 • updated 4 months ago by swbarnes2 ♦ 4.5k
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How to keep sample name while using samtools mpileup + varscan to do variant call?
varscan samtools mpileup written 4 months ago by MatthewP • 20 • updated 4 months ago by Pierre Lindenbaum ♦ 114k
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Can you get mpileup to report positions with coverage of 0?
samtools mpileup written 4 months ago by blur • 90 • updated 4 months ago by Devon Ryan ♦ 86k
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Samtools mpileup returns empty vcf file
samtools mpileup written 4 months ago by shreyasibiswas88 • 30 • updated 4 months ago by RamRS ♦ 19k
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Mpileup generation using Bisulfite converted reference
mpileup faidx samtools bismark bisulfite written 5 months ago by kspata • 40
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Samtools mpileup meaning of IMF and IDV
vcf samtools mpileup written 3.2 years ago by cruckert8 • 10 • updated 5 months ago by elzedleeu • 0
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Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
rpb variant mpileup snp call written 5 months ago by Macspider • 2.6k • updated 5 months ago by al.bodrug • 50
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Creating a Zebrafish reference genome for use by mpileup
vcf variant calling faidx rna-seq mpileup written 6 months ago by dominicdhall • 40
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samtools mpileup output only contains vcf header
variant calling samtools mpileup written 6 months ago by s102060125 • 10 • updated 6 months ago by swbarnes2 ♦ 4.5k
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metagenomic assembly coverage, for multiple samples
bowtie2 metagenomics samtools coverage mpileup written 6 months ago by willnotburn • 40
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Clarification on Bedtools Intersect Usage
bedtools intersect samtools mpileup bam written 7 months ago by Noam Teyssier • 10 • updated 7 months ago by Kevin Blighe ♦ 32k
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mpilup output quality
quality scores samtools mpileup phred33 written 7 months ago by mluypaert • 10
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error while using " samtools mpileup " function
headers read_group samtools mpileup error written 9 months ago by ricfoz • 20 • updated 9 months ago by Devon Ryan ♦ 86k
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7 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 21 months ago by Rob • 90 • updated 9 months ago by Biostar ♦♦ 20
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Why does mpileup tell me the starting and ending base of a read?
samtools mpileup written 21 months ago by Peavil • 10 • updated 9 months ago by Vasisht • 150
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mpileup for PacBio reads
quiver calling pacbio mpileup variants written 19 months ago by Biomonika (Noolean) ♦ 3.0k • updated 11 months ago by tjduncan • 190
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Changing samtools mpileup I16 calculations?
i16 samtools mpileup written 11 months ago by emilywynn6 • 0
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trouble understanding what a warning means while building a .bcf file with samtools
.vcf .bcf samtools mpileup bcftools written 11 months ago by ricfoz • 20 • updated 11 months ago by Devon Ryan ♦ 86k
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Samtools mpileup: AF1 and DP4 not provided
samtools mpileup af1 info written 11 months ago by filippo.martignano • 10 • updated 11 months ago by Kevin Blighe ♦ 32k
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Calling SNPs with low coverage
vcf low-coverage samtools mpileup snp written 19 months ago by devin.porter92 • 0 • updated 12 months ago by pierre.peterlongo • 830
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