Closed jielab closed 6 years ago
reedacartwright
commented
6 years ago It works as expected. dng dnm can process paired and trio samples in a single run. You get 0 Paired samples interrogated because you are using a trio. The SNP and INDEL reports refer to your trio. See below for the section of code responsible.
This is a duplicate of #266.
jielab
commented
6 years ago Dear Reed:
Sorry to bug you on this. If you say that “it works as expected”, where is the analysis results? I did not get any output except that LOG file. Again, I am expecting a report that lists all de-novo mutations based on my trio WES data.
Best regards,
Jie
From: Reed A. Cartwright notifications@github.com Sent: 2018年6月27日 16:36 To: denovogear/denovogear denovogear@noreply.github.com Cc: jiehuang001 jiehuang001@gmail.com; Author author@noreply.github.com Subject: Re: [denovogear/denovogear] Total number of Paired sample sites interrogated: 0 (#279)
It works as expected. dng dnm can process paired and trio samples in a single run. You get 0 Paired samples interrogated because you are using a trio. The SNP and INDEL reports refer to your trio. See below for the section of code responsible.
This is a duplicate of #266 https://github.com/denovogear/denovogear/issues/266 .
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reedacartwright
commented
6 years ago For starters, you might not have any de novo mutations in your data. Try using -c 0 to see if you get any calls.
jielab
commented
6 years ago Dear Reed:
I now downloaded the latest version of DNG, and changed my sample to the new format as below.
18-CG-15-07932_S5_R1_001 . . male =
18-CG-15-07931_S4_R1_001 . . female =
18-CG-15-07930_S3_R1_001 18-CG-15-07932_S5_R1_001 18-CG-15-07931_S4_R1_001 male =
However, now when I run dng dnm auto --rd_cutoff 0 -c 0 --ped sample.ped --bcf trio.bcf, I got the following error:
BCF PARSING ERROR - Unable to find trio!
Members missing: 3!
Skipping site10008
Below, I use bcftools to show that these 3 samples specified in my sample file do exist.
bcftools query -l trio.bcf
18-CG-15-07930_S3_R1_001
18-CG-15-07931_S4_R1_001
18-CG-15-07932_S5_R1_001
Best regards,
Jie
From: Reed A. Cartwright notifications@github.com Sent: 2018年6月27日 17:02 To: denovogear/denovogear denovogear@noreply.github.com Cc: jiehuang001 jiehuang001@gmail.com; Author author@noreply.github.com Subject: Re: [denovogear/denovogear] Total number of Paired sample sites interrogated: 0 (#279)
For starters, you might not have any de novo mutations in your data. Try using -c 0 to see if you get any calls.
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reedacartwright
commented
6 years ago The dng dnm program doesn't support the new ped format. It was designed for the newer dng call program.
jielab
commented
6 years ago Dear Reed:
I now convert back to my old ped file then. Again, the ped file is pasted below. I am not sure that it is OK for me to use “1” as family ID for all 3 persons.
1 18-CG-15-07932_S5_R1_001 0 0 1 0
1 18-CG-15-07931_S4_R1_001 0 0 2 0
1 18-CG-15-07930_S3_R1_001 18-CG-15-07932_S5_R1_001 18-CG-15-07931_S4_R1_001 1 1
Sorry that I have been taking too much of your time. I am not trying to do anything complicated at all. I simply want to use DNG to process a trio dataset and show me a list of variants that are potentially de-novo.
I first used the command samtools mpileup -t DP -gf hg19.fa 18-CG-15-07930_S3_R1_001.bam 18-CG-15-07931_S4_R1_001.bam 18-CG-15-07932_S5_R1_001.bam > trio.bcf to create the VCF file.
Then I use dng dnm auto --rd_cutoff 0 -c 0 --ped sample.ped --bcf trio.bcf.
However, after I run the above two commands, I got NO output files. As you know, it is not possible that there are no de-novo variants in my WGS data. I manually checked the VCF file, and found a lot of variant with AA in father, AC in mother, while CG in proband. Variants like this should be caught as potentially do-novo correct?
As you saw, I have now spent more than 2 months struggling to make this thing work, which is supposed to be very simple. If somehow my data is corrupted, can you please point me to a nice example code and example dataset that analysis of trio works?
Thank you & best regards,
Jie
From: Reed A. Cartwright notifications@github.com Sent: 2018年6月28日 13:33 To: denovogear/denovogear denovogear@noreply.github.com Cc: jiehuang001 jiehuang001@gmail.com; Author author@noreply.github.com Subject: Re: [denovogear/denovogear] Total number of Paired sample sites interrogated: 0 (#279)
The dng-dnm doesn't support the new ped format. It was designed for the newer dng-call program.
On Thu, Jun 28, 2018, 10:07 jiehuang001 <notifications@github.com mailto:notifications@github.com > wrote:
Dear Reed:
I now downloaded the latest version of DNG, and changed my sample to the new format as below.
PEDNG v1.0
Individual Father Mother Sex Samples
18-CG-15-07932_S5_R1_001 . . male =
18-CG-15-07931_S4_R1_001 . . female =
18-CG-15-07930_S3_R1_001 18-CG-15-07932_S5_R1_001 18-CG-15-07931_S4_R1_001 male =
However, now when I run dng dnm auto --rd_cutoff 0 -c 0 --ped sample.ped --bcf trio.bcf, I got the following error:
BCF PARSING ERROR - Unable to find trio!
Members missing: 3!
Skipping site10008
Below, I use bcftools to show that these 3 samples specified in my sample file do exist.
bcftools query -l trio.bcf
18-CG-15-07930_S3_R1_001
18-CG-15-07931_S4_R1_001
18-CG-15-07932_S5_R1_001
Best regards,
Jie
From: Reed A. Cartwright <notifications@github.com mailto:notifications@github.com > Sent: 2018年6月27日 17:02 To: denovogear/denovogear <denovogear@noreply.github.com mailto:denovogear@noreply.github.com > Cc: jiehuang001 <jiehuang001@gmail.com mailto:jiehuang001@gmail.com >; Author <author@noreply.github.com mailto:author@noreply.github.com%0b
Subject: Re: [denovogear/denovogear] Total number of Paired sample sites interrogated: 0 (#279)
For starters, you might not have any de novo mutations in your data. Try using -c 0 to see if you get any calls.
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reedacartwright
commented
6 years ago If you have manually identified sites that are de novos, please post the entire #CHROM header line and entire line from those positions so I can manually inspect them an figure out why they weren't being called.
Hi, guys: I previously posted this question. I was really frustrated that it was not resolved, while I thought that my question is very very simple. I hope that this time i will get better luck. Basically, I have a trio, with 3 BAM files for them. I created a sample.ped file with the following content: 1 18-CG-15-07932_S5_R1_001 0 0 1 0 1 18-CG-15-07931_S4_R1_001 0 0 2 0 1 18-CG-15-07930_S3_R1_001 18-CG-15-07932_S5_R1_001 18-CG-15-07931_S4_R1_001 1 1
Then I run DNG with the following commands: module load samtools/1.8 samtools mpileup -t DP -gf /share/pkg/bwa/ref/hg19.fa ../bam/18-CG-15-07930_S3_R1_001.bam ../bam/18-CG-15-07931_S4_R1_001.bam ../bam/18-CG-15-07932_S5_R1_001.bam > trio.bcf module load bcftools bcftools view -Oz -o trio.vcf.gz trio.bcf module load gcc/7.2.0 module load python/2.7.13 module load denovogear/2018-05-1_6723027 dng dnm auto --rd_cutoff 0 --ped sample.ped --bcf trio.bcf
However, instead of getting any output, I got the following LOG file without anything else. Why at the end of this LOG file it says "Total number of Paired sample sites interrogated: 0". I am analyzing a trio, not a pair!!!
[mpileup] 3 samples in 3 input files