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<prev • 181 results • page 1 of 7 • next >
6
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1
answer
130
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1
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Samtools/bcftools force-calling using an input set of variants
variant calling vcf samtools bcftools written 8 days ago by floris.barthel • 20
0
votes
0
answers
49
views
0
answers
reformat forward and reverse read pairs for variant analysis of exons
variant calling assembly exon capture gene written 15 days ago by kspata • 40
1
vote
1
answer
95
views
1
answer
DP and DP at site do not match using only 1 sample in VCF
vcf variant calling gatk written 4 weeks ago by ajuiwl • 30
0
votes
2
answers
150
views
2
answers
Best practices for variant calling on multiple sequencing runs of the same sample
variant calling vcf snps written 5 weeks ago by Damian Kao ♦ 15k • updated 5 weeks ago by swbarnes2 ♦ 4.5k
6
votes
4
answers
827
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6 follow
4
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What is the advantage of variant calling using RNA-seq technique?
variant calling galaxy rna-seq written 5 months ago by akilabioinfo • 0 • updated 5 weeks ago by jpuntomarcos • 10
4
votes
1
answer
118
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1
answer
4/6 genotype in VCF
vcf variant calling genotype written 6 weeks ago by ajuiwl • 30 • updated 6 weeks ago by Pierre Lindenbaum ♦ 114k
4
votes
0
answers
374
views
0
answers
Help with Sanger Imputation Service
variant calling imputation rna-seq written 10 weeks ago by sandKings • 10
1
vote
1
answer
204
views
1
answer
Sanger Imputation Service - The input file sanity check failed : faidx_fetch_seq failed at JH636052.4:4111085
rnaseq variant calling written 10 weeks ago by sandKings • 10
1
vote
1
answer
241
views
1
answer
Hard filtering results of vcf file for multiple samps
variant calling gatk hard filtering written 3 months ago by seta • 1.0k • updated 3 months ago by finswimmer ♦ 6.8k
1
vote
1
answer
202
views
1
answer
Applying BQSR before running GATK's HaplotypeCaller on whole-genome sequencing data
variant calling haplotypecaller written 3 months ago by seta • 1.0k • updated 3 months ago by finswimmer ♦ 6.8k
0
votes
2
answers
175
views
2
answers
Extracting Variants from large set of variants
variant calling vcf wgs data written 3 months ago by bioinfo355 • 0 • updated 3 months ago by ammar.husami • 0
3
votes
1
answer
216
views
1
answer
variant calling after reference genome is updated
variant calling wgs snp written 4 months ago by prasundutta87 • 260
14
votes
1
answer
409
views
6 follow
1
answer
Generate VCF file from csv/excel file
variant calling R vcf python sequencing written 4 months ago by daianagan • 10
1
vote
0
answers
140
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0
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How to get all variants in original BAM file with HaplotypeCaller? (No correction and BAMout)
variant calling haplotypecaller bamout sequencing written 4 months ago by mhmtgenc85 • 30
3
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0
answers
204
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0
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Tool to do Variant calling from contigs data
variant calling contigs written 4 months ago by de.mecquenem.ninon • 10
1
vote
1
answer
192
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1
answer
Find variants supported by at least 20 reads freebayes
variant calling freebayes written 5 months ago by kspata • 40 • updated 5 months ago by finswimmer ♦ 6.8k
1
vote
1
answer
147
views
1
answer
Can DiscoSNP++ deal with hybrid input of both paired-end and single-end reads?
discosnp++ variant calling snp discosnp written 5 months ago by emeline.a.favreau • 0 • updated 5 months ago by pierre.peterlongo • 830
6
votes
2
answers
258
views
5 follow
2
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How do variant callers get genotype info?
variant calling indel snp phasing written 5 months ago by afzm • 20 • updated 5 months ago by Jeremy Leipzig ♦ 18k
4
votes
0
answers
249
views
0
answers
Variant calling on single sample Macaque WGS data - advice please
variant calling haplotypecaller pon mutect2 written 5 months ago by YaGalbi • 1.4k
2
votes
0
answers
295
views
0
answers
Creating a cell by SNP matrix
variant calling bcftools snp genotyping written 5 months ago by dominicdhall • 40
0
votes
0
answers
184
views
0
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Please provide me your comments on the variant calling in this case
variant calling genome sequencing written 5 months ago by seta • 1.0k
1
vote
0
answers
191
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0
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A weird variant call from VarScan2 mpileup2snp
mpileup2snp variant calling varscan2 written 5 months ago by rayliu0115 • 0
7
votes
2
answers
332
views
2
answers
Bcftools view. FREQ inclusion error.
freq annovar bcftools variant calling written 6 months ago by tcom111 • 10
0
votes
0
answers
277
views
0
answers
Best way to call low-frequency SNVs in antibody sequence from FASTQ
variant calling alignment antibody snp written 5 months ago by maquino1985 • 0
2
votes
1
answer
278
views
1
answer
Creating a Zebrafish reference genome for use by mpileup
vcf variant calling faidx rna-seq mpileup written 6 months ago by dominicdhall • 40
2
votes
1
answer
306
views
1
answer
Can I use different versions of dbsnp for variant calling using GATK and variant annotation?
variant calling gatk dbsnp variant annotation written 6 months ago by dolevrahat • 10 • updated 6 months ago by finswimmer ♦ 6.8k
0
votes
0
answers
238
views
0
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Mappability in duplicate gene?
variant calling exome sequencing written 6 months ago by Tania • 120
2
votes
1
answer
219
views
1
answer
Please suggest your idea for variant calling analysis of many BAM files from whole genome sequencing
variant calling alingnment whole genome sequencing written 6 months ago by seta • 1.0k • updated 6 months ago by finswimmer ♦ 6.8k
3
votes
2
answers
300
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2
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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
3
votes
1
answer
750
views
1
answer
Strategy in WGS variant calling using GATK (CombineGVCF step)
variant calling gatk snp wgs written 6 months ago by prasundutta87 • 260
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