User: Molly_K

gravatar for Molly_K
Molly_K40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 days, 10 hours ago
Joined:
4 years, 3 months ago
Email:
k******@gmail.com

Posts by Molly_K

<prev • 14 results • page 1 of 2 • next >
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Comment: C: bcftools filtering INFO column issues (empty output)
... Hi Pierre, I used the following command line and noticed a drop in the row numbers > bcftools view -e '(R2<0 || R2>=0)' $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz > test1.vcf wc -l chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz 1176573 chr22_rsq_filtered.vcf_remov ...
written 17 days ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... I apologize for the weird behaviour of the file. I think after copy paste from the terminal there are some tabs missing. Here's a link to the first 100 rows of the vcf file that I extracted bcftools view $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz | head -100 > $FILE/test2.vcf h ...
written 17 days ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... Updated the original post to fit in the first 19 rows. It's the header + the first snp. If I don't limit the row number, it would keep running till the end of the file. Thanks. ...
written 18 days ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... Hi Pierre, here's the output [filter.c:2278 filters_init1] Error: the tag "GQ_MEAN" is not defined in the VCF header ...
written 18 days ago by Molly_K40
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bcftools filtering INFO column issues (empty output)
... How can I filter out variants with R2!="." in the INFO column? > bcftools view -i 'INFO/R2!="."' -Oz $FILE -o $OUTFILTERED The above generated a vcf.gz file with only the header. I have used the same command line to filter VCF file based on the R2 score and it worked fine. Just wondering what ...
vcf filter bcftools missing info written 18 days ago by Molly_K40
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Comment: C: Genotype input in matrix eqtl with dosage dataset
... This is highly inappropriate. Thanks but no thank. ...
written 26 days ago by Molly_K40
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Genotype input in matrix eqtl with dosage dataset
... I have performed eQTL with matrix eQTL tool before with hard call genotype. I wonder if anyone has tried with dosage genotype. The data format is SNP A1 A2 F1 I1 F2 I2 F3 I3 rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01 rs0002 G A 0.00 1.00 ...
dosage genotype eqtl written 26 days ago by Molly_K40 • updated 26 days ago by devidjohn470
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Comment: C: michigan imputation server
... Hi Teresa, I am interested in if you have found a way to solve the problem with the dosage data. I wonder what did you do with your DosageConvertor output file? How did you QC on that? Thanks! ...
written 4 weeks ago by Molly_K40
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Answer: A: how to unzip Michigan imputation server output compressed folder
... The imputation server encrypts all zip files by default using the 256-bit key. The standard unzip program does not work, you will need to install 7-Zip program. Once you have the program, type in the following: 7z e file.zip Then enter your password. ...
written 4 weeks ago by Molly_K40
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Comment: C: vcftools: unwanted filtering
... I basically realized it's a misunderstanding on my end so I deleted the question, realizing it isn't even a good question, but if someone has the same doubt when interpreting the results, this post may be helpful :P ...
written 9 months ago by Molly_K40

Latest awards to Molly_K

Scholar 9 months ago, created an answer that has been accepted. For C: vcftools: unwanted filtering
Popular Question 22 months ago, created a question with more than 1,000 views. For Permutation using Plink

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