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<prev • 195 results • page 1 of 7 • next >
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From mpileup on bam files to TMB calculation, how is it done?
snps bam mutations mpileup tmb written 2 hours ago by Pin.Bioinf • 230
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143
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Multimapping reads intervention in SNP calling
alignment samtools snp mpileup written 9 weeks ago by sambioinfo2018 • 0 • updated 22 hours ago by Biostar ♦♦ 20
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How do I calculate the total read depth and allele frequency using just the target bed file and aligned bam
bed frequency allele mpileup bam written 3.6 years ago by bobrowdy123 • 0 • updated 7 days ago by Biostar ♦♦ 20
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Mpileup Segmentation Fault
mpileup written 6.5 years ago by AW • 350 • updated 17 days ago by Biostar ♦♦ 20
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203
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SNP calling using samtools
rnaseq samtools bcftools snp mpileup written 5 weeks ago by ankit4035hinsu • 10 • updated 25 days ago by Biostar ♦♦ 20
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getting the HOM_REF genotypes using bcftools mpileup+call ?
bcftools variant call mpileup genotype written 26 days ago by Pierre Lindenbaum ♦ 116k • updated 26 days ago by RamRS ♦ 20k
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231
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Variant Calling (Samtools Mpileup): Error
variant calling samtools bcftools mpileup written 6 weeks ago by venuraherath • 20
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350
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5 follow
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Confused about how to generate a consensus sequence after bwa
samtools bwa mpileup written 10 weeks ago by DNAngel • 20
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254
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1
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bcftools mpileup no output (empty calls.bcf file)
consensus bcftools samtools mpileup calls.bcf written 10 weeks ago by RobertUt • 10
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bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
bcftools samtools mpileup snp wgs written 10 weeks ago by serpalma.v • 20
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I16 Info Tag
bcftools snp mpileup sequencing written 10 weeks ago by tbb21 • 10 • updated 10 weeks ago by finswimmer ♦ 9.9k
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12 follow
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How To Create A Venn Diagram Of Sample1.Vcf, Sample2.Vcf And Sample1&2(Union).Vcf Files
vcftools mpileup written 7.1 years ago by Deniz • 50 • updated 3 months ago by zx8754 ♦ 6.5k
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400
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How to read an mpileup file from Samtools into Python
python next-gen samtools mpileup written 4 months ago by M.O.L.S • 0
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213
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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 3 months ago by claudiadast • 0
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1
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163
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How to read my Samtools mpileup?
samtools student mpileup written 4 months ago by c.clarido • 40 • updated 4 months ago by finswimmer ♦ 9.9k
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208
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1
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Samtools mpileup genotype likelihood no PL field when all individuals are 0/0
pl samtools mpileup written 4 months ago by cetin.m • 20 • updated 4 months ago by Santosh Anand ♦ 4.6k
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bcftools mpileup output format
bcftools mpileup written 5 months ago by tarek.mohamed • 240
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275
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How to add sequence information to vcf from MPileup
vcf bam snp mpileup rna-seq written 5 months ago by helge.fluess • 0
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Bcftools view options for SNPs calling.
bcftools samtools snp mpileup written 3.6 years ago by Eddie_I • 20 • updated 6 months ago by Kevin Blighe ♦ 37k
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213
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1
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Order of samtools mpileup - arbitrary or not?
samtools mpileup written 6 months ago by blur • 90 • updated 6 months ago by Devon Ryan ♦ 88k
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1
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378
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1
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Calculate average mapping quality at a position
mapping quality mpileup written 6 months ago by hpapoli • 70 • updated 6 months ago by Gabriel R. • 2.5k
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285
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samtools mpileup `error uninitialized value $l in numeric lt` during BAM to FASTA conversion
fasta samtolls mpileup bam written 7 months ago by marongiu.luigi • 360
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1
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7 follow
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Samtools mpileup degenerative characters
samtools degenrative characters mpileup written 19 months ago by bruseq • 20 • updated 7 months ago by swbarnes2 ♦ 4.8k
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403
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How to keep sample name while using samtools mpileup + varscan to do variant call?
varscan samtools mpileup written 7 months ago by MatthewP • 60 • updated 7 months ago by Pierre Lindenbaum ♦ 116k
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5 follow
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Can you get mpileup to report positions with coverage of 0?
samtools mpileup written 7 months ago by blur • 90 • updated 7 months ago by Devon Ryan ♦ 88k
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Samtools mpileup returns empty vcf file
samtools mpileup written 8 months ago by shreyasibiswas88 • 30 • updated 8 months ago by RamRS ♦ 20k
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288
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Mpileup generation using Bisulfite converted reference
mpileup faidx samtools bismark bisulfite written 8 months ago by kspata • 40
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Samtools mpileup meaning of IMF and IDV
vcf samtools mpileup written 3.5 years ago by cruckert8 • 20 • updated 9 months ago by elzedleeu • 20
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286
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Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
rpb variant mpileup snp call written 9 months ago by Macspider • 2.7k • updated 9 months ago by al.bodrug • 50
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352
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1
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Creating a Zebrafish reference genome for use by mpileup
vcf variant calling faidx rna-seq mpileup written 9 months ago by dominicdhall • 40
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