User: donfreed

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donfreed1.4k
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Bioinformatics Scientist at Sentieon (www.sentieon.com).

Posts by donfreed

<prev • 69 results • page 1 of 7 • next >
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Comment: C: Modifying fasta file based on vcf information
... This is working perfectly for me. Thanks! ...
written 12 months ago by donfreed1.4k
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Comment: C: how to distinguish mosaicism out of germline de novo mutations
... I would not use readbackedphasing. If I recall correctly, it does not take advantage of the paired read information. Also, it will not work because it doesn't understand somatic variants. For the phasing, yes you can try to phase each de novo variant to a nearby heterozygous germline variant, but g ...
written 12 months ago by donfreed1.4k
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Answer: A: how to distinguish mosaicism out of germline de novo mutations
... You should probably use another technique to confirm that the variants are either germline *de novo* or mosaic. Here are a few possibilities: 1. **Single-cell sequencing.** If a variant is absent from some of the cells, this is good evidence that that variant is mosaic and not *de novo*. 2. **Hap ...
written 12 months ago by donfreed1.4k
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Answer: A: Mutect 2 on WGS data takes too long to run
... You can try the Sentieon Genomic Tools: http://www.biorxiv.org/content/early/2017/05/12/115717. We provide a variant caller (TNhaplotyper, part of TNseq) that provides matching results to MuTect2 with a substantial performance improvement. You can request a free trial from https://www.sentieon.com/h ...
written 18 months ago by donfreed1.4k
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Answer: A: How to find variants that are common in one population but rare in others (popul
... You can do this pretty easily using the GATK assuming that your VCF has the `AF` info field annotation. First annotate the variants in your VCF with the allele frequency of the variants in 1000 Genomes. java -jar $GATK -R reference.fasta -T VariantAnnotator -V input.vcf -o output_1.vcf --resour ...
written 2.1 years ago by donfreed1.4k
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Comment: C: I want to store a docker image reproducing a paper. Is there a host for docker i
... You can upload the data to AWS and then make the bucket containing the data [requester pays.][1] If you do this you will only get a flat fee for data storage and you will not pay data transfer fees when others access the data. [1]: http://docs.aws.amazon.com/AmazonS3/latest/dev/RequesterPaysBuck ...
written 2.5 years ago by donfreed1.4k
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Comment: C: gVCF files from 1000 Genomes samples
... Thanks for the info. Our study is focused on rare variation so in our case sample breadth (more samples) is more important than having the properties of variants in our samples exactly match our control population, which is why we are performing analysis of the low-coverage samples. We do not have t ...
written 2.7 years ago by donfreed1.4k
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gVCF files from 1000 Genomes samples
... We are hoping to use 1000 Genomes samples as a population control for our study. The 1000 Genomes Project provides fastq, BAM and VCF files on their ftp site. We do not want to use VCF files as they have been filtered and might not contain variants occurring in our samples (especially false-positive ...
1000 genomes gvcf written 2.7 years ago by donfreed1.4k • updated 2.7 years ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: samtools vcf output disagree with mpileup in DP
... Have you tried the `-A` flag? From the docs: "-A, --count-orphans Do not skip anomalous read pairs in variant calling." ...
written 3.0 years ago by donfreed1.4k
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Answer: A: A command line option for region in GenotypeGVCFs?
... From https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_engine_CommandLineGATK.php#--intervals: " --intervals / -L One or more genomic intervals over which to operate Use this option to perform the analysis over only part of the genome. This argument can be specified multi ...
written 3.0 years ago by donfreed1.4k

Latest awards to donfreed

Appreciated 7 months ago, created a post with more than 5 votes. For A: Validated CNV dataset for NA12878
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: What are chimeric reads?
Scholar 7 months ago, created an answer that has been accepted. For A: python subprocesses and wrappers for Jce tool
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Is it possible to reconstruct alignment from CIGAR and MD strings alone?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Get Reference file from BAM
Popular Question 8 months ago, created a question with more than 1,000 views. For Calculation of PFBs for CNV analysis from 1000 Genomes data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is it possible to reconstruct alignment from CIGAR and MD strings alone?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: what is crude blood
Scholar 12 months ago, created an answer that has been accepted. For A: python subprocesses and wrappers for Jce tool
Student 15 months ago, asked a question with at least 3 up-votes. For gVCF files from 1000 Genomes samples
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: what is crude blood
Autobiographer 18 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 20 months ago, created a question with more than 1,000 views. For Calculation of PFBs for CNV analysis from 1000 Genomes data
Guru 22 months ago, received more than 100 upvotes.
Scholar 2.1 years ago, created an answer that has been accepted. For A: python subprocesses and wrappers for Jce tool
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For gVCF files from 1000 Genomes samples
Student 2.7 years ago, asked a question with at least 3 up-votes. For gVCF files from 1000 Genomes samples
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: What read lengths are produced by modern Illumina sequencers?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Tool for random access to indexed BAM files in S3?
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: What read lengths are produced by modern Illumina sequencers?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What read lengths are produced by modern Illumina sequencers?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What read lengths are produced by modern Illumina sequencers?

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