User: MAPK

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MAPK1.7k
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Posts by MAPK

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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 11 minutes 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 9 days 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 17 days 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 18 days 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 7 weeks 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 8 weeks ago by MAPK1.7k • updated 8 weeks ago by ATpoint44k
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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 8 weeks ago by MAPK1.7k
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Answer: A: Split paired end fastq per lane from a bam file
... If someone wants awk solution, I also have written this. This also creates RG files. #!/bin/bash SM=SAMPLE DNA=BARCODE PR=PROJECT FULLSM="SM^DNA^PR" ### splitfq1.sh set -x echo "Splitting lanes from FASTQ: ${FQ_OUT1}" awk -v sm="$SM" -v dna="$DNA" -v pr="$ ...
written 9 weeks ago by MAPK1.7k
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Comment: C: Split paired end fastq per lane from a bam file
... I ended up using this `demuxbyname.sh`. I found it very fast- takes only 15 minutes to split 200G fastq. But before doing this, I did: `samtools collate -uO ${INBAM} | samtools fastq - -@ ${THREADS} -N -1 ${FQ_OUT1} -2 ${FQ_OUT2} -0 /dev/null -s /dev/null -n` . It would be nice if they had an optio ...
written 9 weeks ago by MAPK1.7k
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Comment: C: How to assign read groups to bam files?
... @swbarnes2 No I was just guessing if batch correction is needed even within the same flowcells. I have not tested it yet, but I was told to do RG per lane in my lab. ...
written 10 weeks ago by MAPK1.7k

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Popular Question 3 days ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
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Epic Question 3 months ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
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