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<prev • 228 results • page 1 of 8 • next >
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How do I know bcftools mpileup command completed?
dna-seq bcftools mpileup written 6 days ago by townsendae • 0
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1
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Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
ngs bam samtools mpileup written 7.9 years ago by tsk • 10 • updated 10 days ago by aroob.lab • 0
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111
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9 follow
1
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Calling triovariants using varscan from a compressed mileup file ?
trio varscan samtools mpileup pipe written 7 weeks ago by dare_devil • 1.4k • updated 6 weeks ago by svp • 420
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4.4k
views
1
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error with vcfutils when building consensus sequence with samtools and bcftools 1.2
vcfutils samtools mpileup consensus sequence written 6.0 years ago by cheng • 20 • updated 7 weeks ago by aebrahimi58 • 0
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How do I make a fasta reference file from a set of bam files in order to maximize the number of heterozygotes in my reference genome?
vcfutils samtools bcftools mpileup seqtk written 3 months ago by fabiopertille • 0 • updated 9 weeks ago by Biostar ♦♦ 20
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14k
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14 follow
4
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Extract Base Based On Position From Bam File
samtools mpileup written 8.7 years ago by Empyrean • 160 • updated 4 months ago by nickhir • 30
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198
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1
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bcftools mpileup create an empty output file
bcftools bam samtools mpileup bwa written 4 months ago by Assa Yeroslaviz • 1.4k
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2
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13 follow
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Best Practices / Faster Samtools Mpileup, Any Tips?
samtools mpileup written 8.7 years ago by Kevin • 640 • updated 6 months ago by wljlinksly • 50
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Weird Samtools Mpileup Error In Mplp_Func.
samtools mpileup error written 7.4 years ago by Shellfishgene • 60 • updated 6 months ago by Emad • 0
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1
answer
752
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1
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MAPQ mapping quality
snp mpileup call written 7 months ago by sami • 20
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244
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1
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mpileup error : Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
mpileup written 7 months ago by sami • 20
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difference between bcftools mpileup and bcftools call
bcftools variant call mpileup written 7 months ago by sami • 20
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SNPs and DEL/MNP in the same position. (DEL or SNP ??)
vcf indels calls snp mpileup written 7 months ago by sami • 20 • updated 7 months ago by Ram ♦ 32k
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1
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202
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1
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Why does samtools mpileup skip positions?
samtools mpileup written 7 months ago by m.wekking • 10 • updated 7 months ago by Istvan Albert ♦♦ 86k
0
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1
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245
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1
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Error on pysam.bcftools.mpileup: "Segmentation fault (core dumped)"
bcftools samtools pysam mpileup written 7 months ago by sbstevenlee • 0
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232
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samtools mpileup -l gives the wrong REF base for some positions
samtools mpileup written 9 months ago by oconnwald • 20
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317
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1
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Bcftools Mpileup bias for alternative alleles?
gatk bcftools mpileup snp written 9 months ago by cetin.m • 50 • updated 9 months ago by Kevin Blighe ♦ 71k
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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 4.0 years ago by cristian • 260 • updated 9 months ago by Biostar ♦♦ 20
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4.9k
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5 follow
3
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Per Sample Mpileup Output From Merged Bam File
samtools mpileup written 7.2 years ago by thomasvangurp • 10 • updated 10 months ago by wkretzsch • 0
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samtools mpileup on mitochondrial bam results in incorrect base quality scores
mitochondria samtools mpileup base-quality written 10 months ago by gmora • 30
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462
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1
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Generate VCF from different .bam files with different chromosome names
vcf bcftools mpileup written 11 months ago by ctdarwell • 0 • updated 11 months ago by Kevin Blighe ♦ 71k
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2
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7.1k
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2
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samtools mpileup - how to extract the alternative allele counts for *each* alternative base
samtools alt mutation mpileup written 5.0 years ago by Michi • 970 • updated 12 months ago by Ks-seq • 10
5
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1
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286
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1
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Exclamation mark in Samtools mpileup output
bam samtools mapping mpileup written 12 months ago by pr • 10 • updated 12 months ago by gb • 1.9k
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Convert VCF to mpileup/synchronized format
vcf popoolation tool synchronized format mpileup written 12 months ago by aniqaejaz220 • 30
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5 follow
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How to parallelize bcftools mpileup with GNU parallel?
parallel bcftools mpileup written 13 months ago by beausoleilmo • 370
11
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1
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6 follow
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What is the difference between mpileup samtools and bcftools?
variant calling bcftools samtools mpileup snp written 13 months ago by beausoleilmo • 370 • updated 13 months ago by jkbonfield • 490
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in bcftools mpileup output, the DP number is not equal to depth in I16 tag
i16 bcftools mpileup written 15 months ago by wm • 490 • updated 15 months ago by harold.smith.tarheel • 4.6k
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Shall I change bcftools mpileup max depth?
variant calliing bcftools sampling mpileup written 16 months ago by marongiu.luigi • 520
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bcftools mpileup with --region option output wrong consequence
bam bcftools mpileup snp written 16 months ago by SSK • 10
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626
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1
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How to reconstruct reads or bam file from pileup
alignment samtools mpileup bam written 17 months ago by SSK • 10 • updated 17 months ago by h.mon ♦ 32k
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