User: quachtina96

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quachtina9640
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United States
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4 years, 1 month ago
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4 years, 3 months ago
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Posts by quachtina96

<prev • 16 results • page 1 of 2 • next >
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GATK CombineVCF How to order the genotypes/samples?
... Hi,  I am trying to merge 3 VCFs (one for each sample) into a single VCF, and I would like them to be listed  in a specific order (proband, mother, father).  How can I specify this to GATK CombineVariants? I've tried inputting the arguments in order, with the first variant given by me being proba ...
multiple samples gatk combining vcf written 4.1 years ago by quachtina9640
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Comment: C: Unusual samtools mpileup output?
... 1) The fai file is one kb and it only contains chrRCRS 16569 9 70 71 2) If I'm interpreting this correctly, the chromosome name is the same in the header (See below) @HD VN:1.4 GO:none SO:coordinate @SQ SN:chrRCRS LN:16569 @RG ID:ID18_Father PL:ILLUMINA PU:L0 ...
written 4.2 years ago by quachtina9640
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Unusual samtools mpileup output?
... Hi, I am using samtools mpileup to generate a pileup file, and my output doesn't match the example pileup files I've seen (e.g. the example on  the pileup format article on Wikipedia). Do you agree that there seems to be something wrong with my file? If so, any suggestions on how to fix it? The co ...
variant calling mtdna samtools mpileup written 4.2 years ago by quachtina9640 • updated 4.0 years ago by Biostar ♦♦ 20
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Picard AddOrReplaceReadGroups unable to read my argument?
... Hi, I am trying to run Picard's AddOrReplaceReadGroups on a bam file called exome_mtExtractremap.csort.bam (code below). the error messages states "ERROR: Option 'RGPL' is required.", however I have included RGPL, so I don't understand why it is occuring. I've tried RGLB=ILLUMINA, RGLB="ILLUMINA", ...
picard read group written 4.2 years ago by quachtina9640
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Comment: C: samtools sort remapped bam by readname/query name
... Hi Pierre! I am using samtools depth, not mpileup. Does this change your answer? ...
written 4.2 years ago by quachtina9640
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samtools sort remapped bam by readname/query name
... Hi, I extracted mitochondrial reads from a bam file and remapped them to a reference genome through the following python function (remap2mt). my goal is to take this bam file (remapped) and find the depth of coverage for that bam file (samtools depth -r chrM remapped.bam) . This requires the bam fi ...
bam samtools sort written 4.2 years ago by quachtina9640 • updated 4.2 years ago by Pierre Lindenbaum123k
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Comment: C: Bedtools bamtofastq error
... Yes, I did sort the BAM file by read name before running the command. I am not sure if my situation is different because the bam I am working with is only the mtDNAextract bam and thus is just the chrM. The rest of the header is there from when I extracted the bam with header (came from the bam from ...
written 4.2 years ago by quachtina9640
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Comment: C: Bedtools bamtofastq error
... Hi Devon! You were right. I put in on the left of bamToFastq instead of the right! But I have one more question:With the following command,  bamToFastq -i mtExtract.qsort.bam -fq firsttestfile.fq -fq2 secondtestfile.fq I got the following in the output: *****WARNING: Query D3NJ6HQ1:424:HA49WADX ...
written 4.2 years ago by quachtina9640
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Bedtools bamtofastq error
... Hi, I am trying to convert my bam file into two fastq files in the command line, but I run into an error and I'm not sure what to change/do differently. Thoughts/advice? my line: bedtools bamtofastq ID18_Father_exome_L001_001_mtExtract.qsort.bam -fq test1.fq -fq2 test2.fq the error:   ***** ...
bedtools bamtofastq fastq bam written 4.2 years ago by quachtina9640
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Extracted the chrM portion of bam into a new bam with header
... Hello,  I used  samtools view -b -h exome.bam chrM > extractedchrM.bam to extract the mitochondrial DNA from an exome into a bam file and to include a header. I was wondering if the header below was correct considering that my new bam is only chrM, but the header has more than that.  Is it be ...
header samtools chrm bam written 4.2 years ago by quachtina9640 • updated 4.2 years ago by Gabriel R.2.6k

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