User: MAPK

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MAPK1.7k
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Posts by MAPK

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Comment: C: Combine two VCF files with GATK4
... @devarora they (MergeVcfs) both are same, either you use via GATK or Picard. I get the same error. ...
written 6 weeks ago by MAPK1.7k
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Comment: C: Combine two VCF files with GATK4
... @dare_devil The samples in file1.vcf.gz and file2.vcf.gz are different (like I said, this is what I want to combine), so this is the error I am getting: [Sun Jan 17 22:03:33 CST 2021] MergeVcfs --INPUT File1.vcf.gz --INPUT File2.vcf.gz --OUTPUT OUTfile.vcf.gz --VERBOSITY INFO --QUIET false - ...
written 6 weeks ago by MAPK1.7k
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Combine two VCF files with GATK4
... Hi All, I have been trying to combine two VCF files with `file1.vcf` with samples A,B,C and `file2.vcf` with samples D,E,F. I tried tools like GatherVcfs, MergeVcfs, but they both fail. What is the right tool I should be using to do this? There was `CombineVariants` tool in GATK3, which is not avai ...
gatk written 6 weeks ago by MAPK1.7k • updated 6 weeks ago by svp420
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MergeVcfs vs GatherVCFs in GATK 4
... Hi All, I am using GATK after several years. I used to merge chromosomes chr{1..22} chrX and chrY with same samples using catVariants in GATK3. It looks like they have replaced this tool with something different on GATK4. So I would like to confirm if I am using right tools- > 1. Do I use Gathe ...
gatk written 7 weeks ago by MAPK1.7k
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Comment: C: Extract subset of samples from multigenome vcf file
... What would be the equivalent option in current GATK(4.1.2 or latest)? Is it `--sample-name` to extract samples from the wanted list? ...
written 8 weeks ago by MAPK1.7k
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Comment: C: BWA aligner error: paired reads have different names
... I don't have much information on the trimming as I received the samples from sequencing center already trimmed/pre-processed. I ran the pipeline again and this time it worked without making any change which I think is very weid. ...
written 9 weeks ago by MAPK1.7k
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BWA aligner error: paired reads have different names
... Hi All, I was trying to run bwa with paired FASTQ and ran over this problem below. How do I fix this error? Thanks! [mem_sam_pe] paired reads have different names: "HISEQ2000B:573:C6027ACXX:1:2314:18", "HISEQ2000B:573:C6027ACXX:1:2314:18428:92556" Command exited with non-zero status 1 ...
bwa written 9 weeks ago by MAPK1.7k
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Comment: C: Picard throwing error for non-existent file
... I am running this on docker. Do I execute like this? root@WL-05104:/mnt/an/test# docker run -t achalneupane/bam2fq echo /mnt/an/test/${fileName} && ls /mnt/an/test/${fileName} && /usr/local/openjdk-8/bin/java ${JAVAOPTS} -jar /usr/bin/picard.jar RevertSam -I /mnt//test/${fi ...
written 3 months ago by MAPK1.7k
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How to add prefix to samtools collate
... I am trying to run this command in loop. While doing so I am getting error for tmp directory having no space in collate step. I saw that samtools manual mentioning about prefix, but I am not sure how to redirect to temporary files to desired `/path` using prefix. samtools collate -uO ${INBAM} ...
samtools written 3 months ago by MAPK1.7k • updated 3 months ago by ATpoint46k
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Comment: C: PhD in Bioinformatics: to continue, or not to continue? That is the question--
... @khorms Oh, this has been so long. I left that lab and the university. Got my PhD from a different university working with a very helpful PI. I was able to finish my PhD in less three years and I am now working. ...
written 3 months ago by MAPK1.7k

Latest awards to MAPK

Epic Question 23 days ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
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Epic Question 11 weeks ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
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Popular Question 3 months ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For How to extract specific chromosome from vcf file
Appreciated 3 months ago, created a post with more than 5 votes. For R programming: genotype concordance
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Popular Question 5 months ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Appreciated 6 months ago, created a post with more than 5 votes. For R programming: genotype concordance
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Student 7 months ago, asked a question with at least 3 up-votes. For R programming, concatenate or combine all the column contents
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