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345
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What Major Copy Number (MCC) and Copy Number (CN) means for CANVAS
CANVAS VCF
22 months ago by ManuelDB ▴ 80
0
votes
2
replies
573
views
Beedtools intersect unable to open a vcf file
VCF Bedtools
updated 11 months ago by 43k • written 23 months ago by ▴ 80
0
votes
1
reply
368
views
Morbidity inheritance dataset
inheritance Morbidity
updated 24 months ago by 54k • written 24 months ago by ▴ 80
1
vote
1
reply
652
views
What LOH means in CANVAS
CANVAS
updated 24 months ago by ★ 3.2k • written 24 months ago by ▴ 80
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1
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1.1k
views
Comment: Comment: How annotation can be validated
24 months ago by ManuelDB ▴ 80
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0
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1.1k
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Comment: Comment: How annotation can be validated
24 months ago by ManuelDB ▴ 80
0
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0
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287
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Can I infer the Zygosity of a CNV based on the number SNPs call in its region?
CNV
24 months ago by ManuelDB ▴ 80
0
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2
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1.1k
views
Comment: Comment: How annotation can be validated
24 months ago by ManuelDB ▴ 80
4
votes
1
reply
514
views
bedtools interset doesn't return a VCF file?
bedtools
updated 2.1 years ago by ★ 1.8k • written 2.1 years ago by ▴ 80
1
vote
1
reply
1.0k
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 14 months ago by 43k • written 2.1 years ago by ▴ 80
2
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5
replies
1.4k
views
Strange error when using gzip.open with a VCF file
vcf gzip pandas
updated 2.1 years ago by ▴ 20 • written 2.3 years ago by ▴ 80
0
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0
replies
305
views
Overlapping CNVs against NSPs
Bedtools VCF CNV
2.1 years ago by ManuelDB ▴ 80
0
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0
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350
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Does VarScan output work with NGS Benchmarking v1.6.?
VarScan NGS_Benchmarking
2.1 years ago by ManuelDB ▴ 80
0
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1
reply
2.5k
views
Comment: Comment: File write failed (wrong size) when filtering a bam file with interset
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
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0
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2.5k
views
Comment: Comment: File write failed (wrong size) when filtering a bam file with interset
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 80
0
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0
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277
views
How to apply probabilistic method to call variants in a simple example.
Bayes-theorem
2.1 years ago by ManuelDB ▴ 80
0
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1
reply
784
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Comment: Comment: Calling variants after using different read alignment programs
2.1 years ago by ManuelDB ▴ 80
3
votes
3
replies
784
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
1
vote
0
replies
682
views
Comment: Comment: Unexpected results when alignment FASTQ files with different read alignments
2.1 years ago by ManuelDB ▴ 80
0
votes
2
replies
1.5k
views
Comment: Comment: Cannot read non-existent file: when executing MarkDuplicates in a script
2.1 years ago by ManuelDB ▴ 80
0
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0
replies
582
views
Comment: Comment: Bus error (core dumped) when Aligning contigs to the reference in QUAST
2.1 years ago by ManuelDB ▴ 80
0
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0
replies
582
views
Comment: Comment: Bus error (core dumped) when Aligning contigs to the reference in QUAST
2.1 years ago by ManuelDB ▴ 80
0
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3
replies
582
views
Bus error (core dumped) when Aligning contigs to the reference in QUAST
Spades QUAST
2.1 years ago by ManuelDB ▴ 80
0
votes
1
reply
1.8k
views
Comment: Comment: Troubles running IGV on a server.
2.1 years ago by ManuelDB ▴ 80
0
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1
reply
1.8k
views
Comment: Comment: Troubles running IGV on a server.
2.1 years ago by ManuelDB ▴ 80
0
votes
1
reply
1.8k
views
Comment: Comment: Troubles running IGV on a server.
2.1 years ago by ManuelDB ▴ 80
0
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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
0
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0
replies
3.0k
views
Comment: Comment: How do I count the real total reads from a fastq file?
2.1 years ago by ManuelDB ▴ 80
0
votes
1
reply
682
views
Comment: Comment: Unexpected results when alignment FASTQ files with different read alignments
2.1 years ago by ManuelDB ▴ 80
4
votes
4
replies
682
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 2.2 years ago by ★ 2.9k • written 2.2 years ago by ▴ 80
0
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2
replies
2.1k
views
Comment: Comment: Are not all duplicated reads removed when applying removal duplicated algorithms
2.2 years ago by ManuelDB ▴ 80
0
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0
replies
356
views
QUAL cut-off in variants filtering
NGS
2.2 years ago by ManuelDB ▴ 80
0
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0
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327
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
0
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0
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2.3k
views
Comment: Comment: How do you know if a variant is in cis or trans when looking at it with IGV
2.2 years ago by ManuelDB ▴ 80
4
votes
4
replies
2.3k
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
0
votes
1
reply
863
views
Comment: Comment: Why is needed a genome reference when calling variants
2.2 years ago by ManuelDB ▴ 80
5
votes
3
replies
863
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
0
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1
reply
661
views
Comment: Comment: Find a position in IGV when variant is giving in the format gene_name 12345-1G>
2.2 years ago by ManuelDB ▴ 80
1
vote
3
replies
661
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
556
views
Plotting the density of CNV with karyoploteR
karyoploteR
2.2 years ago by ManuelDB ▴ 80
0
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1
reply
1.2k
views
Comment: Comment: How to extract gene name and transcript name from the INFO column of a VCF file
2.3 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 2.3 years ago by ▴ 520 • written 2.3 years ago by ▴ 80
0
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0
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1.4k
views
Comment: Comment: Strange error when using gzip.open with a VCF file
2.3 years ago by ManuelDB ▴ 80
0
votes
3
replies
669
views
Why in Biomart Exon region start is before than Gene start?
Biomart
updated 2.3 years ago by 100k • written 2.3 years ago by ▴ 80
0
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0
replies
528
views
Comment: Comment: iterating over LiftOver in big dataset
2.3 years ago by ManuelDB ▴ 80
0
votes
2
replies
528
views
iterating over LiftOver in big dataset
pyliftover LiftOver
2.3 years ago by ManuelDB ▴ 80
0
votes
0
replies
700
views
Comment: Comment: Unrecognised chromosome value (e.g. chr16_KI270853v1_alt) in the UCSC Genome Bro
2.3 years ago by ManuelDB ▴ 80
4
votes
3
replies
867
views
What the last output of liftover means?
liftover Python
updated 2.3 years ago by ★ 2.0k • written 2.3 years ago by ▴ 80
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