Page 15 of 16 FirstFirst ... 513141516 LastLast
Results 141 to 150 of 154

Thread: Dante Labs WES/WGS Sequencing Technical

  1. #141
    Registered Users
    Posts
    206
    Sex
    Nationality
    Finnish
    Y-DNA (P)
    R1b-Z142
    mtDNA (M)
    H10g

    BioRxiv has a paper about a new mapper called Urmap. "URMAP is an order of magnitude faster than BWA and Bowtie2 with comparable accuracy on a benchmark test using simulated paired 150nt reads of a well-studied human genome."

    https://www.biorxiv.org/content/10.1...01.12.903351v1

    https://github.com/rcedgar/urmap

    Creating an index requires around 41 gigabytes of memory and accessing swap slows it down to a crawl. First tests show it is very fast especially with "veryfast" option but seems to quit without error messages when source data has errors. The author is very busy with Covid-19 related stuff at the moment.

  2. The Following User Says Thank You to teepean47 For This Useful Post:

     aaronbee2010 (06-04-2020)

  3. #142
    Registered Users
    Posts
    69
    Sex
    Location
    Morocco
    Ethnicity
    Berber
    Y-DNA (P)
    E-M81
    mtDNA (M)
    K1a4a1

    Morocco
    Question:

    YSEQ has converted my DanteLabs Fastq files (FASTQ Mapping to hg38) and now I want to get my autosomal dna results with it (like uploading on FTDNA, MyHeritage and other autosomal websites), what step do I need to take? Do I use WGSextract to make the autosomal files out of the BAM file that YSEQ delivered me?

  4. The Following User Says Thank You to Adamm For This Useful Post:

     aaronbee2010 (06-26-2020)

  5. #143
    Registered Users
    Posts
    83
    Sex
    Nationality
    Finnish
    Y-DNA (P)
    I-Y40511
    mtDNA (M)
    U5b1-a2h2d2a1a2

    Finland
    You get better autosomal results if you use the hs37d5 BAM file Dante made for you with WGS extract as those co-ordinates don't have to be lift-overed from hg38->hg19.

  6. The Following User Says Thank You to tontsa For This Useful Post:

     aaronbee2010 (06-26-2020)

  7. #144
    Registered Users
    Posts
    69
    Sex
    Location
    Morocco
    Ethnicity
    Berber
    Y-DNA (P)
    E-M81
    mtDNA (M)
    K1a4a1

    Morocco
    Quote Originally Posted by tontsa View Post
    You get better autosomal results if you use the hs37d5 BAM file Dante made for you with WGS extract as those co-ordinates don't have to be lift-overed from hg38->hg19.
    is that the standard bam file they delivered?

  8. #145
    Gold Class Member
    Posts
    1,220
    Sex
    Location
    Birmingham, UK
    Ethnicity
    Indian - Punjabi Jatt
    Nationality
    British
    Y-DNA (P)
    R2-SK2142 > A26339
    mtDNA (M)
    U7a3a
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a

    England United Kingdom India India Punjab
    Quote Originally Posted by Adamm View Post
    is that the standard bam file they delivered?
    Yes. They include (or at least, they're supposed to include) a hs37d5 BAM file for you alongside your FASTQ and VCF files.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > A26339 - M5a1a
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a
    * MGMs F (?): L-M22 > M357 - ?
    * PGMs F (?): Q-F1096 > F4747 - ?
    * MGMs MGF (?): R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana (?): T-Y11151 > Y13290 - R30b1

    Hidden Content

  9. #146
    Registered Users
    Posts
    69
    Sex
    Location
    Morocco
    Ethnicity
    Berber
    Y-DNA (P)
    E-M81
    mtDNA (M)
    K1a4a1

    Morocco
    Quote Originally Posted by aaronbee2010 View Post
    Yes. They include (or at least, they're supposed to include) a hs37d5 BAM file for you alongside your FASTQ and VCF files.
    Yes thanks, the problem is that WGSExtract doesn't work for that BAM file, when I try to generate a raw file (MyHeritage or 23andMe format) it (the program) just freezes and doesnt do anything. Do you perhaps have a solution to this?

  10. #147
    Gold Class Member
    Posts
    1,220
    Sex
    Location
    Birmingham, UK
    Ethnicity
    Indian - Punjabi Jatt
    Nationality
    British
    Y-DNA (P)
    R2-SK2142 > A26339
    mtDNA (M)
    U7a3a
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a

    England United Kingdom India India Punjab
    Quote Originally Posted by Adamm View Post
    Yes thanks, the problem is that WGSExtract doesn't work for that BAM file, when I try to generate a raw file (MyHeritage or 23andMe format) it (the program) just freezes and doesnt do anything. Do you perhaps have a solution to this?
    Normally, the "please wait" window in WGSExtract is supposed to freeze until the autosomal file is generated. Now, I have an issue that occurs more often than not when I try to generate an autosomal file. The "please wait" window pops up, but when I look at the Windows task manager, I see that nothing is actually happening. Everytime this happens, I have to keep restarting WGSExtract and trying again until I see a "Python" process in my task manager taking around 16.5% of my CPU, which tells me that it's now working. I'm not sure if this is the issue that you may be having?
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > A26339 - M5a1a
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a
    * MGMs F (?): L-M22 > M357 - ?
    * PGMs F (?): Q-F1096 > F4747 - ?
    * MGMs MGF (?): R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana (?): T-Y11151 > Y13290 - R30b1

    Hidden Content

  11. The Following User Says Thank You to aaronbee2010 For This Useful Post:

     Adamm (06-26-2020)

  12. #148
    Registered Users
    Posts
    69
    Sex
    Location
    Morocco
    Ethnicity
    Berber
    Y-DNA (P)
    E-M81
    mtDNA (M)
    K1a4a1

    Morocco
    Quote Originally Posted by aaronbee2010 View Post
    Normally, the "please wait" window in WGSExtract is supposed to freeze until the autosomal file is generated. Now, I have an issue that occurs more often than not when I try to generate an autosomal file. The "please wait" window pops up, but when I look at the Windows task manager, I see that nothing is actually happening. Everytime this happens, I have to keep restarting WGSExtract and trying again until I see a "Python" process in my task manager taking around 16.5% of my CPU, which tells me that it's now working. I'm not sure if this is the issue that you may be having?
    Now I managed to get it work, the problem is that they generate the file but its empty. It only shows this:


  13. The Following User Says Thank You to Adamm For This Useful Post:

     aaronbee2010 (06-26-2020)

  14. #149
    Gold Class Member
    Posts
    1,220
    Sex
    Location
    Birmingham, UK
    Ethnicity
    Indian - Punjabi Jatt
    Nationality
    British
    Y-DNA (P)
    R2-SK2142 > A26339
    mtDNA (M)
    U7a3a
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a

    England United Kingdom India India Punjab
    Quote Originally Posted by Adamm View Post
    Now I managed to get it work, the problem is that they generate the file but its empty. It only shows this:

    I don't recall anything like that happening with me! Did anything suspicious pop up on the command prompt that opens alongside the WGSExtract program?

    Looking at the extract23 bash script that WGSExtract uses internally, the main commands performed therein are:

    1. samtools mpileup -C 50 -v -l ${REF_23ANDME} -f ${REF} ${BAMFILE_SORTED} > 23andMe_raw.vcf.gz (finding and recording parts of the BAM file that correspond to coordinates present in genotyping chips)

    2. bcftools call -O z -V indels -m -P 0 23andMe_raw.vcf.gz > 23andMe_called.vcf.gz (uses certain parameters to make position calls from the previous file [i.e. AA, CT or -- (no-call)])

    3. bcftools annotate -O z -a ${REF_23ANDME} -c CHROM,POS,ID 23andMe_called.vcf.gz > 23andMe_annotated.vcf.gz (adds rsIDs present in chip genotyping files)

    4. bcftools query -f '%ID\t%CHROM\t%POS[\t%TGT]\n' 23andMe_annotated.vcf.gz | sed 's/chr//' | sed 's/\tM\t/\tMT\t/g' | sed 's/\///' | sed 's/\.\.$/--/' | sed 's/TA$/AT/' | sed 's/TC$/CT/' | sed 's/TG$/GT/' | sed 's/GA$/AG/' | sed 's/GC$/CG/' | sed 's/CA$/AC/' > 23andMe_V3_hg19.tab (converts the previous vcf.gz file to a 23andMe-style tabulated file and performs some string replacement using "sed" for compatibility)

    5. sort -t $'\t' -k2,3 -V 23andMe_V3_hg19.tab > 23andMe_V3_hg19_sorted.tab (sorts tabulated file by chromosomal coordinates)

    6. cat header.txt 23andMe_V3_hg19_sorted.tab >> ${OUTFILE} (adds 23andMe-style header to tabulated file)

    All I can see from your picture is that step 6 worked fine, but something appears to have went wrong in at least one of the previous 5 steps. My gut feeling is saying that it's either step 1 or 2 that failed in this case, as the other steps are simplistic in nature and I feel like an error in those steps is a lot less likely to occur. Would you be able to try and get this going again and see what the command prompt says?
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > A26339 - M5a1a
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a
    * MGMs F (?): L-M22 > M357 - ?
    * PGMs F (?): Q-F1096 > F4747 - ?
    * MGMs MGF (?): R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana (?): T-Y11151 > Y13290 - R30b1

    Hidden Content

  15. #150
    Registered Users
    Posts
    69
    Sex
    Location
    Morocco
    Ethnicity
    Berber
    Y-DNA (P)
    E-M81
    mtDNA (M)
    K1a4a1

    Morocco
    Quote Originally Posted by aaronbee2010 View Post
    I don't recall anything like that happening with me! Did anything suspicious pop up on the command prompt that opens alongside the WGSExtract program?

    Looking at the extract23 bash script that WGSExtract uses internally, the main commands performed therein are:

    1. samtools mpileup -C 50 -v -l ${REF_23ANDME} -f ${REF} ${BAMFILE_SORTED} > 23andMe_raw.vcf.gz (finding and recording parts of the BAM file that correspond to coordinates present in genotyping chips)

    2. bcftools call -O z -V indels -m -P 0 23andMe_raw.vcf.gz > 23andMe_called.vcf.gz (uses certain parameters to make position calls from the previous file [i.e. AA, CT or -- (no-call)])

    3. bcftools annotate -O z -a ${REF_23ANDME} -c CHROM,POS,ID 23andMe_called.vcf.gz > 23andMe_annotated.vcf.gz (adds rsIDs present in chip genotyping files)

    4. bcftools query -f '%ID\t%CHROM\t%POS[\t%TGT]\n' 23andMe_annotated.vcf.gz | sed 's/chr//' | sed 's/\tM\t/\tMT\t/g' | sed 's/\///' | sed 's/\.\.$/--/' | sed 's/TA$/AT/' | sed 's/TC$/CT/' | sed 's/TG$/GT/' | sed 's/GA$/AG/' | sed 's/GC$/CG/' | sed 's/CA$/AC/' > 23andMe_V3_hg19.tab (converts the previous vcf.gz file to a 23andMe-style tabulated file and performs some string replacement using "sed" for compatibility)

    5. sort -t $'\t' -k2,3 -V 23andMe_V3_hg19.tab > 23andMe_V3_hg19_sorted.tab (sorts tabulated file by chromosomal coordinates)

    6. cat header.txt 23andMe_V3_hg19_sorted.tab >> ${OUTFILE} (adds 23andMe-style header to tabulated file)

    All I can see from your picture is that step 6 worked fine, but something appears to have went wrong in at least one of the previous 5 steps. My gut feeling is saying that it's either step 1 or 2 that failed in this case, as the other steps are simplistic in nature and I feel like an error in those steps is a lot less likely to occur. Would you be able to try and get this going again and see what the command prompt says?
    Only this happens:



    And it stays like this.

    Normally how long would you need to wait in order for it to generate an autosomal file?

Page 15 of 16 FirstFirst ... 513141516 LastLast

Similar Threads

  1. Dante Labs (WGS)
    By MacUalraig in forum Dante Labs
    Replies: 1222
    Last Post: 06-16-2020, 08:07 PM
  2. Dante Labs WGS (30x) $299
    By noman in forum Dante Labs
    Replies: 0
    Last Post: 03-21-2020, 10:53 PM
  3. Dante Labs subforum?
    By MacUalraig in forum Suggestions
    Replies: 2
    Last Post: 11-11-2019, 12:35 AM
  4. Whole Genome sequence $299 at Dante Labs
    By Dr_McNinja in forum Dante Labs
    Replies: 15
    Last Post: 02-18-2019, 12:30 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •