User: chariko

gravatar for chariko
chariko30
Reputation:
30
Status:
New User
Location:
Spain
Last seen:
3 months ago
Joined:
5 years, 2 months ago
Email:
m****************@gmail.com

Posts by chariko

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Bam file MC tag as integer
... Thank you very much for your anwer @John. You are right this could be an explanation about this MC:i values. In my case, the version of biobambam2 which was run was 2.0.8 which was released in April 2015 When checking issues of biobambam2 they fixed it in version 2.0.58 https://github.com/gt1/bio ...
written 5 months ago by chariko30
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Comment: A: Bam file MC tag as integer
... Thank you very much for your answer. This command makes my MC tag to dissapear and therefore now it does not give any errors when running PIcard, but as you said, I am not sure about the effect this could have. I will check it... I will also try to know in which step of the analysis this value for ...
written 5 months ago by chariko30
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Bam file MC tag as integer
... Hi, I downloaded a bam file and when running Picard ValidateSamFile option I got the following error: ERROR ... ValidateSamFile Value for tag MC is not a String: class java.lang.Integer When looking through the sam file I realized that the MC was as follows: MC:i:1479433 When looking the Sam ...
mc bam validatesamfile sam written 5 months ago by chariko30
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Answer: A: SHAPEIT error after run: x samples are included in several duos/trios
... did you manage to solve your problem? ...
written 10 months ago by chariko30
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... I get the error in the following step: Quality Control Chromosome X check failed! java.io.IOException: Something went wrong with the plink command Error during manifest file creation. Also, I run locallly the steps from the michigan server by downloading from github the code and I also got the er ...
written 2.1 years ago by chariko30
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Answer: A: Imputation of chromosome X using the Michigan imputation server
... Talking with a friend which had the same problem as we, we checked Michigan´s code and the problem was that one of the lines of the code calls plink to check for sex in order to create the 3 files (one for males, another for females and the other for the pseudoautosomal (PAR) zone). Is in this part ...
written 2.2 years ago by chariko30
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Answer: A: Imputation of chromosome X using the Michigan imputation server
... I finally was able to impute also my X chromosome by setting as missing values those heterozygous SNPs from male samples. This heterozigous genotypes are probably due to a bad classification by the genotyping software. In any case, I was able to remove them with plink when creating the vcf files: ...
written 2.3 years ago by chariko30
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Answer: A: Imputation of chromosome X using the Michigan imputation server
... Hi, I am having the same problem when imputing an X chromosome. Did you manage to resolve it? ...
written 2.3 years ago by chariko30
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Answer: A: Negative start position bed file
... Afeter changing the data to 0 and 1, I decided to remove those reads because also the coverage was very low (3x) so I really do not belive the results. Thanks all for your answers. ...
written 4.8 years ago by chariko30
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Comment: C: Negative start position bed file
... thanks for your answer, but... what do you mean off by one error?  would you consider to discard this result and that´s all? thanks again ...
written 4.8 years ago by chariko30

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Negative start position bed file
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