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<prev • 226 results • page 1 of 8 • next >
2
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138
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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 2 days ago by fabiopertille • 0
13
votes
4
answers
14k
views
14 follow
4
answers
Extract Base Based On Position From Bam File
samtools mpileup written 8.4 years ago by Empyrean • 160 • updated 21 days ago by nickhir • 20
1
vote
1
answer
112
views
1
answer
bcftools mpileup create an empty output file
bcftools bam samtools mpileup bwa written 23 days ago by Assa Yeroslaviz • 1.4k
15
votes
2
answers
13k
views
12 follow
2
answers
Best Practices / Faster Samtools Mpileup, Any Tips?
samtools mpileup written 8.4 years ago by Kevin • 640 • updated 3 months ago by wljlinksly • 50
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3
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2.2k
views
3
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Weird Samtools Mpileup Error In Mplp_Func.
samtools mpileup error written 7.1 years ago by Shellfishgene • 50 • updated 3 months ago by Emad • 0
3
votes
1
answer
229
views
1
answer
MAPQ mapping quality
snp mpileup call written 3 months ago by sami • 20
1
vote
1
answer
186
views
1
answer
mpileup error : Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
mpileup written 3 months ago by sami • 20
0
votes
0
answers
166
views
0
answers
difference between bcftools mpileup and bcftools call
bcftools variant call mpileup written 3 months ago by sami • 20
4
votes
0
answers
293
views
0
answers
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
vcf indels calls snp mpileup written 3 months ago by sami • 20 • updated 3 months ago by RamRS ♦ 30k
3
votes
1
answer
157
views
1
answer
Why does samtools mpileup skip positions?
samtools mpileup written 3 months ago by m.wekking • 10 • updated 3 months ago by Istvan Albert ♦♦ 85k
0
votes
1
answer
187
views
1
answer
Error on pysam.bcftools.mpileup: "Segmentation fault (core dumped)"
bcftools samtools pysam mpileup written 4 months ago by sbstevenlee • 0
0
votes
0
answers
181
views
0
answers
samtools mpileup -l gives the wrong REF base for some positions
samtools mpileup written 5 months ago by oconnwald • 20
0
votes
1
answer
222
views
1
answer
Bcftools Mpileup bias for alternative alleles?
gatk bcftools mpileup snp written 6 months ago by cetin.m • 50 • updated 6 months ago by Kevin Blighe ♦ 67k
4
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0
answers
2.6k
views
0
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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 3.7 years ago by cristian • 250 • updated 6 months ago by Biostar ♦♦ 20
3
votes
3
answers
4.8k
views
5 follow
3
answers
Per Sample Mpileup Output From Merged Bam File
samtools mpileup written 7.0 years ago by thomasvangurp • 10 • updated 6 months ago by wkretzsch • 0
0
votes
0
answers
218
views
0
answers
samtools mpileup on mitochondrial bam results in incorrect base quality scores
mitochondria samtools mpileup base-quality written 6 months ago by gmora • 30
0
votes
1
answer
340
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1
answer
Generate VCF from different .bam files with different chromosome names
vcf bcftools mpileup written 8 months ago by ctdarwell • 0 • updated 8 months ago by Kevin Blighe ♦ 67k
9
votes
2
answers
6.7k
views
2
answers
samtools mpileup - how to extract the alternative allele counts for *each* alternative base
samtools alt mutation mpileup written 4.7 years ago by Michi • 970 • updated 9 months ago by Ks-seq • 10
5
votes
1
answer
245
views
1
answer
Exclamation mark in Samtools mpileup output
bam samtools mapping mpileup written 9 months ago by pr • 10 • updated 9 months ago by gb • 1.9k
1
vote
0
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186
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0
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Convert VCF to mpileup/synchronized format
vcf popoolation tool synchronized format mpileup written 9 months ago by aniqaejaz220 • 30
7
votes
2
answers
969
views
2
answers
How to parallelize bcftools mpileup with GNU parallel?
parallel bcftools mpileup written 10 months ago by beausoleilmo • 330
10
votes
1
answer
966
views
6 follow
1
answer
What is the difference between mpileup samtools and bcftools?
variant calling bcftools samtools mpileup snp written 10 months ago by beausoleilmo • 330 • updated 10 months ago by jkbonfield • 430
0
votes
1
answer
336
views
1
answer
in bcftools mpileup output, the DP number is not equal to depth in I16 tag
i16 bcftools mpileup written 12 months ago by wm • 490 • updated 11 months ago by harold.smith.tarheel • 4.6k
0
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0
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308
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0
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Shall I change bcftools mpileup max depth?
variant calliing bcftools sampling mpileup written 12 months ago by marongiu.luigi • 520
0
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0
answers
551
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0
answers
bcftools mpileup with --region option output wrong consequence
bam bcftools mpileup snp written 12 months ago by SSK • 10
0
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1
answer
494
views
1
answer
How to reconstruct reads or bam file from pileup
alignment samtools mpileup bam written 13 months ago by SSK • 10 • updated 13 months ago by h.mon ♦ 31k
1
vote
1
answer
226
views
1
answer
.bam mpileup mapping quality
samtools mapq mpileup sanger fastq written 14 months ago by saar.armon • 0 • updated 14 months ago by jkbonfield • 430
1
vote
1
answer
283
views
1
answer
Consensus sequence from multiple BAM files on a single position
bam samtools mpileup written 14 months ago by Federico Giorgi • 630 • updated 14 months ago by jkbonfield • 430
7
votes
0
answers
681
views
0
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Command line explain
bcftools mpileup written 16 months ago by f1978hp • 30 • updated 16 months ago by finswimmer ♦ 14k
0
votes
0
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396
views
0
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Difference between mpileup and HaplotypeCaller -ERC BP_RESOLUTION
variant calling haplotypecaller mpileup written 16 months ago by CY • 550
<prev • 226 results • page 1 of 8 • next >
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