User: win

gravatar for win
win820
Reputation:
820
Status:
Trusted
Location:
India
Last seen:
1 year, 7 months ago
Joined:
7 years, 9 months ago
Email:
a*******@gmail.com

about me

Posts by win

<prev • 221 results • page 1 of 23 • next >
2
votes
1
answer
1.2k
views
1
answer
Interpreting stats from gnomAD/ ExAC reference population
... Hello, I want to generate stats of various types of statistical information from reference population in gnomAD/ExAC reference population and wanted to know what might be the best way to accomplish this. Could not find any open-source tool/ script online and in some online code repos. Any help in ...
exac written 20 months ago by win820 • updated 19 months ago by manuel.belmadani1.2k
0
votes
0
answers
1.2k
views
0
answers
GATK joint genotyping
... Hi all, i am struggling a bit with preparing a cohort genome vcf file for joint genotyping using GATK. I tried with 30 BAMs from 1000 genomes, and generated a single sample VCF for each, then used GATK CombineVariants and produced a "master" gVCF file. This is not working during variant calling si ...
gatk ngs written 2.1 years ago by win820
2
votes
2
answers
1.3k
views
2
answers
Genomic coordinates for transcripts
... Hi all, i have transcript IDs such as NM_001250.5, NM_000073.2 and many more. I wanted to know how could I get hg19 genomic coordinates for each one. I have tried this on UCSC genome browser and wanted to know if it can be automated. any pointers in this direction could be most helpful. thanks ...
ngs written 2.1 years ago by win820 • updated 2.1 years ago by michael.ante3.6k
0
votes
0
answers
659
views
0
answers
Comment: C: VariantRecalibration step issue
... Thanks you very much. I will do as suggested. ...
written 2.1 years ago by win820
0
votes
1
answer
903
views
1
answers
Comment: C: Reference allele is too long message GATK
... same message, it seems like the --reference_window_stop is not working or has incorrect values. ...
written 2.1 years ago by win820
0
votes
1
answer
903
views
1
answers
Comment: C: Reference allele is too long message GATK
... No, thats the problem. ...
written 2.1 years ago by win820
0
votes
1
answer
903
views
1
answers
Comment: C: Reference allele is too long message GATK
... OK, but there are other such messages as well, same message but differing length like some say 108, some are 150 etc. I have also set --reference_window_stop to 1000. ...
written 2.1 years ago by win820
1
vote
1
answer
903
views
1
answer
Reference allele is too long message GATK
... hi all, i generated a gVCF file using HaplotypeCaller. When i run ValidateVariants from GATK i get the message "Reference allele is too long (108) at position chr9:99423855; skipping that record. Set --reference_window_stop >= 108" Any ideas what is causing this? Command used to generate the g ...
vcf written 2.1 years ago by win820 • updated 2.1 years ago by WouterDeCoster43k
0
votes
0
answers
659
views
0
answers
VariantRecalibration step issue
... Hi all, i need some advice about VariantRecalibration as in if I am doing the right thing. Downloaded 30 bams from 1000 genomes and realigned them to HG38. Then using HaplotypeCaller generated a gVCF for each BAM. Then used CombineGVCFs and made a single VCF named cohort.g.vcf Took a sample BAM an ...
vcf written 2.1 years ago by win820
0
votes
0
answers
2.0k
views
0
answers
Comment: A: QD Annotation error in GATK in VariantRecalibration step
... Any ideas as to why this is happening? ...
written 2.1 years ago by win820

Latest awards to win

Great Question 2.1 years ago, created a question with more than 5,000 views. For Promoter Or Enhancer Regions Bed Format
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Generate GVF file from VCF file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For BAM to individual chromosome fasta/fastq
Appreciated 2.1 years ago, created a post with more than 5 votes. For Samtools And Region List
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Great Question 2.1 years ago, created a question with more than 5,000 views. For Create A Tbi File From Vcf
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Reference genome in VCF format (gVCF)
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For Remove Vcf Header Lines
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Length of sequences in FASTQ file
Great Question 2.1 years ago, created a question with more than 5,000 views. For Lift-over on a VCF
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Get Reference file from BAM
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Per chromosome gVCF
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Convert GVF to VCF
Popular Question 2.1 years ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Create A Tbi File From Vcf
Popular Question 2.6 years ago, created a question with more than 1,000 views. For genome coordinates for snps
Epic Question 2.6 years ago, created a question with more than 10,000 views. For Annotate A Vcf File
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Human GRCh38 and dbSNP VCF and GATK
Popular Question 2.6 years ago, created a question with more than 1,000 views. For HG18 coordinates of rs#
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Sample Exome Fastq Files
Great Question 3.0 years ago, created a question with more than 5,000 views. For Sample Exome Fastq Files
Appreciated 3.0 years ago, created a post with more than 5 votes. For Samtools And Region List

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1432 users visited in the last hour