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0
votes
1
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222
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PEAR seems to have sense to me
PEAR
updated 6 weeks ago by 142k • written 6 weeks ago by ▴ 80
0
votes
0
replies
149
views
MultiGemini is not doing indel realignment, right?? Gemini does't work with single read?
MultiGemini
10 weeks ago by ManuelDB ▴ 80
0
votes
1
reply
221
views
FastaAlternateReferenceMaker merges overlapping regions
FastaAlternateReferenceMaker
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 80
1
vote
3
replies
495
views
CIGAR and query sequence lengths differ
pysam samtools
4 months ago by ManuelDB ▴ 80
1
vote
1
reply
391
views
How to properly mock a (Pysam) read
pysam
updated 4 months ago by 100k • written 4 months ago by ▴ 80
2
votes
1
reply
430
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools softclip
updated 5 months ago by ▴ 270 • written 5 months ago by ▴ 80
1
vote
1
reply
281
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
5 months ago by ManuelDB ▴ 80
5
votes
10
replies
832
views
Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ
picard
6 months ago by ManuelDB ▴ 80
5
votes
4
replies
704
views
FASTQ to BAM to CRAM to FASTQ
Samtools
6 months ago by ManuelDB ▴ 80
0
votes
4
replies
1.4k
views
Cannot read non-existent file: when executing MarkDuplicates in a script
GATK4
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 80
0
votes
0
replies
242
views
ERROR::INVALID_ALIGNMENT_START Alignment start should be 0 because reference name = *.
Pysam ValidateSamFile
6 months ago by ManuelDB ▴ 80
1
vote
3
replies
545
views
How to deal with reads which CIGAR is [0-9]+S
CIGAR ampliconclip
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 80
3
votes
2
replies
992
views
Liftover GRCh37 to hg38 1kg/GATK.
Liftover
7 months ago by ManuelDB ▴ 80
5
votes
2
replies
663
views
samtools ampliconclip option --strand is not working?
samtools ampliconclip
8 months ago by ManuelDB ▴ 80
4
votes
7
replies
954
views
How is the format of the bed file for samtools ampliconclip
samtools ampliconclip
updated 8 months ago by ▴ 270 • written 8 months ago by ▴ 80
1
vote
1
reply
435
views
How to mark as QC fail reads with specific CIGARs
BAM PISCES
updated 8 months ago by 100k • written 8 months ago by ▴ 80
5
votes
3
replies
805
views
Why do the same genetic variants sometimes result in different amino acids in the REVEL table?
REVEL
updated 8 months ago by 4.2k • written 8 months ago by ▴ 80
0
votes
0
replies
404
views
Pisces doesn't like high-quality reads when there is a soft-clip affecting the full read.
Pisces
updated 8 months ago by 87k • written 8 months ago by ▴ 80
0
votes
0
replies
312
views
Error processing chr 'chr7': Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968
PISCES
8 months ago by ManuelDB ▴ 80
9
votes
13
replies
1.4k
views
From primers sequence to Bed file
bedtools bwa
9 months ago by ManuelDB ▴ 80
2
votes
2
replies
590
views
I don't really understand what fold mean means
coverage
updated 11 months ago by 43k • written 11 months ago by ▴ 80
5
votes
9
replies
1.7k
views
6 follow
Count regions that overlap with python
CNV
updated 21 months ago by 35k • written 21 months ago by ▴ 80
0
votes
0
replies
342
views
What Major Copy Number (MCC) and Copy Number (CN) means for CANVAS
CANVAS VCF
22 months ago by ManuelDB ▴ 80
0
votes
2
replies
565
views
Beedtools intersect unable to open a vcf file
VCF Bedtools
updated 10 months ago by 43k • written 23 months ago by ▴ 80
0
votes
1
reply
364
views
Morbidity inheritance dataset
inheritance Morbidity
updated 23 months ago by 54k • written 23 months ago by ▴ 80
1
vote
1
reply
645
views
What LOH means in CANVAS
CANVAS
updated 23 months ago by ★ 3.2k • written 23 months ago by ▴ 80
0
votes
0
replies
285
views
Can I infer the Zygosity of a CNV based on the number SNPs call in its region?
CNV
23 months ago by ManuelDB ▴ 80
4
votes
1
reply
505
views
bedtools interset doesn't return a VCF file?
bedtools
updated 2.0 years ago by ★ 1.7k • written 2.0 years ago by ▴ 80
1
vote
1
reply
993
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 13 months ago by 43k • written 2.0 years ago by ▴ 80
2
votes
5
replies
1.4k
views
Strange error when using gzip.open with a VCF file
vcf gzip pandas
updated 2.0 years ago by ▴ 20 • written 2.2 years ago by ▴ 80
0
votes
0
replies
303
views
Overlapping CNVs against NSPs
Bedtools VCF CNV
2.0 years ago by ManuelDB ▴ 80
0
votes
0
replies
345
views
Does VarScan output work with NGS Benchmarking v1.6.?
VarScan NGS_Benchmarking
2.1 years ago by ManuelDB ▴ 80
1
vote
5
replies
2.5k
views
File write failed (wrong size) when filtering a bam file with interset
bedtools
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 80
0
votes
0
replies
273
views
How to apply probabilistic method to call variants in a simple example.
Bayes-theorem
2.1 years ago by ManuelDB ▴ 80
3
votes
3
replies
759
views
Calling variants after using different read alignment programs
Bowtie2 IGV BWA
updated 2.1 years ago by ★ 2.9k • written 2.1 years ago by ▴ 80
0
votes
3
replies
573
views
Bus error (core dumped) when Aligning contigs to the reference in QUAST
Spades QUAST
2.1 years ago by ManuelDB ▴ 80
0
votes
7
replies
1.8k
views
Troubles running IGV on a server.
IGV
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 80
4
votes
4
replies
678
views
Unexpected results when alignment FASTQ files with different read alignments
Bowtie2 BWE
2.1 years ago by ManuelDB ▴ 80
8
votes
10
replies
2.1k
views
6 follow
Are not all duplicated reads removed when applying removal duplicated algorithms?
ngs FASTQC
updated 2.1 years ago by ★ 2.9k • written 2.1 years ago by ▴ 80
0
votes
0
replies
353
views
QUAL cut-off in variants filtering
NGS
2.1 years ago by ManuelDB ▴ 80
0
votes
0
replies
322
views
What is the relationship between the per-base sequence quality of a FASTQ file and the QUAL of a VCF file
NGS
2.2 years ago by ManuelDB ▴ 80
4
votes
4
replies
2.2k
views
How do you know if a variant is in cis or trans when looking at it with IGV
IGV
2.2 years ago by ManuelDB ▴ 80
5
votes
3
replies
860
views
Why is needed a genome reference when calling variants
NGS
updated 2.2 years ago by 142k • written 2.2 years ago by ▴ 80
1
vote
3
replies
649
views
Find a position in IGV when variant is giving in the format gene_name 12345-1G>A
igv
updated 2.2 years ago by ▴ 190 • written 2.2 years ago by ▴ 80
0
votes
0
replies
554
views
Plotting the density of CNV with karyoploteR
karyoploteR
2.2 years ago by ManuelDB ▴ 80
1
vote
3
replies
1.2k
views
How to extract gene name and transcript name from the INFO column of a VCF file
pandas VCF
updated 2.2 years ago by ▴ 520 • written 2.2 years ago by ▴ 80
0
votes
3
replies
656
views
Why in Biomart Exon region start is before than Gene start?
Biomart
updated 2.2 years ago by 100k • written 2.2 years ago by ▴ 80
0
votes
2
replies
520
views
iterating over LiftOver in big dataset
pyliftover LiftOver
2.2 years ago by ManuelDB ▴ 80
4
votes
3
replies
857
views
What the last output of liftover means?
liftover Python
updated 2.2 years ago by ★ 2.0k • written 2.2 years ago by ▴ 80
1
vote
1
reply
504
views
How to see how long a command takes in Galaxy?
Galaxy
updated 2.2 years ago by ▴ 180 • written 2.2 years ago by ▴ 80
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