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<prev • 215 results • page 1 of 8 • next >
0
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Generate VCF from different .bam files with different chromosome names
vcf bcftools mpileup written 13 days ago by ctdarwell • 0 • updated 10 days ago by Kevin Blighe ♦ 56k
7
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2
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5.6k
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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 4.1 years ago by Michi • 950 • updated 5 weeks ago by Ks-seq • 10
6
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1
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92
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1
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Exclamation mark in Samtools mpileup output
bam samtools mapping mpileup written 6 weeks ago by pr • 10 • updated 6 weeks ago by gb • 1.7k
1
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0
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67
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0
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Convert VCF to mpileup/synchronized format
vcf popoolation tool synchronized format mpileup written 7 weeks ago by aniqaejaz220 • 30
7
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2
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210
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2
answers
How to parallelize bcftools mpileup with GNU parallel?
parallel bcftools mpileup written 9 weeks ago by beausoleilmo • 300
7
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1
answer
149
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1
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What is the difference between mpileup samtools and bcftools?
variant calling bcftools samtools mpileup snp written 9 weeks ago by beausoleilmo • 300 • updated 9 weeks ago by jkbonfield • 350
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1
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146
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1
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in bcftools mpileup output, the DP number is not equal to depth in I16 tag
i16 bcftools mpileup written 4 months ago by wm • 350 • updated 3 months ago by harold.smith.tarheel • 4.5k
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0
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117
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0
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Shall I change bcftools mpileup max depth?
variant calliing bcftools sampling mpileup written 4 months ago by marongiu.luigi • 490
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0
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214
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0
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bcftools mpileup with --region option output wrong consequence
bam bcftools mpileup snp written 5 months ago by SSK • 10
0
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1
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248
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1
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How to reconstruct reads or bam file from pileup
alignment samtools mpileup bam written 6 months ago by SSK • 10 • updated 6 months ago by h.mon ♦ 29k
1
vote
1
answer
162
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1
answer
.bam mpileup mapping quality
samtools mapq mpileup sanger fastq written 6 months ago by saar.armon • 0 • updated 6 months ago by jkbonfield • 350
1
vote
1
answer
191
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1
answer
Consensus sequence from multiple BAM files on a single position
bam samtools mpileup written 6 months ago by Federico Giorgi • 590 • updated 6 months ago by jkbonfield • 350
7
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0
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418
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0
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Command line explain
bcftools mpileup written 8 months ago by f1978hp • 30 • updated 8 months ago by finswimmer ♦ 13k
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0
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195
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0
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Difference between mpileup and HaplotypeCaller -ERC BP_RESOLUTION
variant calling haplotypecaller mpileup written 8 months ago by CY • 470
4
votes
1
answer
292
views
1
answer
Samtools mplileup detects wrong INDEL positions
variant calling samtools count nuceotides mpileup written 8 months ago by vit.filippo • 40 • updated 8 months ago by finswimmer ♦ 13k
0
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1
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274
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1
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How to calculate allele counts(Ref and alt) using a target bed file and aligned bam sample files
count allele samtools rna-seq mpileup written 9 months ago by prernagoel04 • 0 • updated 9 months ago by H.Hasani • 880
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0
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683
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0
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Samtools mpileup with 10x data
samtools mpileup written 10 months ago by lali1 • 0
3
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1
answer
239
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1
answer
Unexpected characters at consensus fasta generated by mpileup
samtools consensussequence mpileup written 10 months ago by gokberk • 60
2
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2
answers
678
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2
answers
Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
rpb variant mpileup snp call written 22 months ago by Macspider • 3.0k • updated 10 months ago by al.bodrug • 50
1
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0
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558
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0
answers
bcftools mpileup --max depth : What would be a reasonable setting for this option?
consensus bcftools mpileup written 11 months ago by Cookie-san • 80
0
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1
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349
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1
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Samtools mpileup - Sudden decrease of coverage at homopolymer regions
samtools mapping mpileup written 11 months ago by Louis Kok • 20 • updated 11 months ago by Kevin Blighe ♦ 56k
0
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0
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333
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0
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Are both samtools mpileup options -m and -F only related to indel detection?
next-gen alignment samtools mpileup snp written 13 months ago by serpalma.v • 30
0
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0
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399
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0
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From mpileup on bam files to TMB calculation, how is it done?
snps bam mutations mpileup tmb written 13 months ago by Pin.Bioinf • 270
0
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0
answers
602
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0
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Multimapping reads intervention in SNP calling
alignment samtools snp mpileup written 15 months ago by sambioinfo2018 • 0 • updated 13 months ago by Biostar ♦♦ 20
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1
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3.1k
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1
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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 4.8 years ago by bobrowdy123 • 0 • updated 13 months ago by Biostar ♦♦ 20
1
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2
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3.5k
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2
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Mpileup Segmentation Fault
mpileup written 7.6 years ago by AW • 350 • updated 14 months ago by Biostar ♦♦ 20
0
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0
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635
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0
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SNP calling using samtools
rnaseq samtools bcftools snp mpileup written 15 months ago by ankit hinsu • 10 • updated 14 months ago by Biostar ♦♦ 20
2
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0
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765
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0
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getting the HOM_REF genotypes using bcftools mpileup+call ?
bcftools variant call mpileup genotype written 14 months ago by Pierre Lindenbaum ♦ 127k • updated 14 months ago by RamRS ♦ 26k
3
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0
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964
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0
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Variant Calling (Samtools Mpileup): Error
variant calling samtools bcftools mpileup written 15 months ago by venuraherath • 20
5
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0
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1.6k
views
6 follow
0
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Confused about how to generate a consensus sequence after bwa
samtools bwa mpileup written 16 months ago by DNAngel • 40
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