search

Illumina / paragraph

Graph realignment tools for structural variants
Other
150 stars 28 forks source link

Trouble genotyping lifted variants #55

Closed Parsoa closed 3 years ago

Parsoa commented 4 years ago

I have a VCF of SVs in GRCh38, but I need to genotype a number of samples mapped to GRCh37. Remapping the samples is not an option. I converted my original variants from VCF to BED by just keeping the CHROM, BEGIN and END (from INFO) fields. I then lifted the BED file using UCSC and updated the VCF file with new coordinates (only BEGIN and END will change).

Paragraph could genotype the original calls without problem but it crashes when trying to genotype the lifted. I created a new VCF file with only 10 of the SVs and passed that to Paragraph to try to figure out what's wrong. Here's the error I get:

2020-10-13 16:44:49,884 WARNING  chr1:114350134 Padding base in genome is different from VCF. Use the one from genome.
2020-10-13 16:44:54,586 ERROR    Traceback (most recent call last):
2020-10-13 16:44:54,586 ERROR      File "/share/binaries/Paragraph/bin/multigrmpy.py", line 315, in run    subprocess.check_call(commandline, shell=True, stderr=subprocess.STDOUT)
2020-10-13 16:44:54,587 ERROR      File "/software/anaconda3/4.5.12/lssc0-linux/lib/python3.6/subprocess.py", line 311, in check_call    raise CalledProcessError(retcode, cmd)
2020-10-13 16:44:54,587 ERROR    subprocess.CalledProcessError: Command '/share/binaries/Paragraph/bin/grmpy --response-file=/tmp/tmpzmne8osh.txt' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/share/binaries/Paragraph/bin/multigrmpy.py", line 353, in <module>
    main()
  File "/share/binaries/Paragraph/bin/multigrmpy.py", line 349, in main
    run(args)
  File "/share/binaries/Paragraph/bin/multigrmpy.py", line 315, in run
    subprocess.check_call(commandline, shell=True, stderr=subprocess.STDOUT)
  File "/software/anaconda3/4.5.12/lssc0-linux/lib/python3.6/subprocess.py", line 311, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/share/hormozdiarilab/Codes/NebulousSerendipity/binaries/Paragraph/bin/grmpy --response-file=/tmp/tmpzmne8osh.txt' returned non-zero exit status 1.

The SVs being genotyped (original coordinates):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  GENOTYPE        2:GENOTYPE      3:GENOTYPE
chr1    59605   INS0000 C       <INS>   30      .       END=59605;SVTYPE=INS;SEQ=tttcttttttttttttttttttttttgaggagttccttgtcgccgctgggtggcggcgcgattgctcctgcagctccgcccccgtccccattcctgcctcgcctcccaagtactggactcagcgccccctcgcccggctaatttttgtatttttagtaagacgtttccgtttagcggggttcgatctctgacttcgtgtcctccgcctcgctcccagtgtgattacagCTGACCACCCCCCCAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60       GT      ./.     ./.     ./.
chr1    181325  DEL0000 G       <DEL>   30      .       END=181448;SVTYPE=DEL;SEQ=GCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCACAGGCGCAGAGACACATGCTAGCGCGCCCAGGGGAGGAGGCGTggcgcaggcgcagagaggcgcgCCGTGCTG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60       GT      ./.     ./.     ./.
chr1    191407  INS0001 A       <INS>   30      .       END=191407;SVTYPE=INS;SEQ=TGTCTCTAGCACCTGGGATGGGCCTGATGTGTAACAGCTGCTGGCTGAACAGAAAGtgacagatgagcaaacatctcaaggaggtgatgaggatggtgatgagtgagaactcccgacatgtgaagataactgaagatgttctggctaaagatccgaagactctaagaatatgatcattccctttgaatatcaaatatcaaaagggctgtcaggtggagaagtgagtaaacttgtatcagaatagcggcagagTTGCAAGGAAACAGATCTCTGTTCTGTTAAAAAAAAAAAATTCCATAAACAACTGCATCACTTTGCATAGCAATTAGGTTCCAGCTCACAAGCGCCTTCCGGGGTGCCCCAAGGGTGAATCCTGCTAAGGTGGAGGTAGAAGACATGACCCTGGGGCTCTTTCCTTAGCCAAGAGCCCATGAGACTAAGGAACATCGTGCTTGTTGACAAAGACCCCGGACAGTCTATTCTCTTACGGTCACAGGCTATGGTGCCAAGGACAAGTGCAGACTCAGGATCAGAAAGCTTGCAGCATATCTGCTATCTCCATGGATAGCAGGATGGTCTGGAAGGCTGTGTCGGAAGGCCCTTAGGCCTCACTGGGGCCAGGCCGTTGATGAACAATGTCCACCCTGAGGGTCGGGAATGGTGCCATTTGTTTGTCATTCCTGGTCCAGACGCCCTTGGCTTGGTGGCTACTCAAGTAGGTCAGTTTACAAGCTCAGTGCTGAACCCATACCCTATGGCACGCTCGCCAGCACTAGAGAGGAAGCTGCCTCTGTGGACATCAGGGACGGAAGTGGCTCACCCAGCCTGTTCTGCGCGTGTCTCACTAAGGGTCCATCTTCCTCTATCTGCCCCGGAGGGGACCATCTCCAAGCATCCCTTGCTTTCCTTCTCCCCCCTCCACCCTCACTGTTCAATAACTTGAGTGCATCCCATTTGTAGAGCACATGCTGGGCCGTGGAGTGAAAGACAATCAGACGACACACATCCACATTCAAAGGGACTCAGGGCTCCTGGGAAGTAGAAATGAATATCAATAACCAAACATCCCacagcctgggtttcacatctgtttagcagcaggtgaccctggggaggtcactaactggtctctgcctcagcttcttccactgaaaaacaggaatggtcccttctacatcatggatactgtgaggTGAGAAGGAGCTGATCATGGCCCATCAACCTCAGCACACCAGTCCCCCTAGAGGCTGCTGGGAGAAGAAGCAGGGAGCACCCACTCCTGACCCAGATTCACATTCACTGCTCTCCTCCCCTGCCTCTGTCATGACCCCAGGGAAGCAGACGCTGAACCTGGGCTCTTGCCTTCATCTTTATCTTCTCCACTCTGGGATAATTAAGAATGACTTGCTAATTATGCAGATCTAGTGCAATGTGTAACTTCGGGCCACCAGTGCCAATCAGTAGAGCGGAGATGACGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaTCAAATCAATTTAAAAAACAATAAACTCCACCACCTCCCCCCTCACCCTCCCGTCATCTGCACTGATTTGTTCTCCCGGGAGCTGGAGAGGAGGGGGGGGGGGCAGCG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60   GT      ./.     ./.     ./.
chr1    710579  INS0002 T       <INS>   30      .       END=710579;SVTYPE=INS;SEQ=AAAGAACTGCCCGCCggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagatcgagaccatcccggctaaaacggtgaaacccgtctctactaaaaatacaaaaattagccgggcgtagtggcggcgcctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagccgagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaa;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60        GT      ./.     ./.     ./.
chr1    732377  INS0003 A       <INS>   30      .       END=732377;SVTYPE=INS;SEQ=GACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCAGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTACATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGCGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTCTTTTTTAGAAAATTGAACAAGTGCTCCCTGTGGTGGCACATACCTCGAGGAtgggaggcagggtggaagggtcacttgaggccattagtttgacaccagcctggccaacaaagtgagaccccgtgtctacaaacaatttaaaaattagccaagtatcgtcatgtatacctacagtcccagctaTCTGAACTTACTGAGAATGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGGCTCATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCTGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttgcattattacactgtaatatataataaaataattatagaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggatggtcccacctgagcgtgatgggagaaagtgacagatcaataggtattagattctcataaggacagcgcaacctagatccctcacatgcacggttcacaacagggtgcgttctcctatgagaatctaacgctgctgctcatctgagaaggtggagctcaggcgggaatgtgagcaaaggggagtggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtggctccttgcggctccatggctcaggggttggggacccctgCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAAGGGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCGGGAAACCAAACCTATGCCCAAATCCATCTGTGTGGGTGTATCTCCTGGGACCCTTCCTAACAtattagtcagagtccaatcaggaagcataaaccactcaaaagtttaaagtggtaaaatttaatacagagaattattcattgtaacaggtgaacagcataatgagagattggctagcacaaagtaaacagaactctagagaatataggactagcCCAggccaggcatggtggctcaggcctgaaattccagcaatttgagaagctaatgcaggaggattgcttaaggccaggagctagagaccggtctggacgacacagtgagaccctgtctctatccaaaagaagaaaaaagttagctgggggtggtagtgcacacttgtagtcccagctactcggaatgcggaagtttgagcctgggaggtcaaggctgcagtgaggcatgattatgccactacagtccagcctggtgacagagcaagaccctgtctcaaagaacaaaaCAACAACAACCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTgaaatgtgacaagtaaagtaatatgagttcttttgtctatgtaaaataatcaaacaaaaaatgacttactaaattataataccctgtgctggcaaaggtgcagtgaaatgggcaccttcttatactatgaggggtgtttaaattgtgtataagccttcccgggtaaagcctgtcaattttttaaaataatggagacagggtctcaccatactgccatactgcctcctccaactcttggcctcaagcaatcctcctctcttagcctcccaaagtgctaagattatagctgggaggcaccCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAACAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACttttttgttgttttgagacagggtctcactctgtcacccaggctggagtgcagaggcctgatcatgactcactgcagtctcagcctccctgggctcaagtgatcctcccacctcagcctcccaagtagctgggactacaggaacatgccaccacactaggctaattcatgtatttttctgtagggatggtgactccccctttgtttccaaggcctatcgcaaactcttggcctcaagccatcctcctgcctcagcctcccaaagtgttgcgattaccagtgtgagccaccacacctggccAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCCACAGCATAATTGTAAAAACATATAGTCgtcgtccctcagtatacagaattagttccagccccccatctctgcatataccaaaatccatgcttactcacgtttcgctgtcacccctctagaatccacgtatacgaaaattccaaatgttagttgggcatagtggcaagcacctgtagtctcagccacgtgggaggttgaggtgggaggatcgcttcagcctggaaggttgaggctgcagtcagctgcgatagcactactacactccagccttggacaacagagggagaccctgtctcagaaaaaaaacaaaataaaaCAGGTTAGAAATTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAAAGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGACTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60        GT      ./.     ./.     ./.
chr1    737102  INS0004 G       <INS>   30      .       END=737102;SVTYPE=INS;SEQ=GGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCGGGAAACCAAACCTATGCCCAAATCCCATCTGTGTGGGTGTATCTCCTGGGACCCTTCCTAACAtattagtcagagtccaatcaggaagcataaaccactcaaaagtttaaagtggtaaaatttaatacagagaattattcattataacaggtgaacagcataatgagagattggctagcacaaagtaaacagaactctagagaatatggactagcCCAggccaggcatggtggctcagcctgaaattccagcaatttgagaagctaatgcaggaggattgcttaaggccaggagctagagaccggtctggacgacacagtgagaccctgtctctatccaaaagaagaaaaaagttagctgggggtggtagtgcacacttgtagtcccagctactcggaatgcgaagtttgagcctgggaggtcaaggctgcagtgaggcatgattatgccactacagtccagcctggtgacagagcaagacctgtctcaaagaacaaaacaacaacaaCCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTgaaatgtgacaagtaaagtaatatgagttcttttgtctatgtaaaataatcaaacaaaaaatgacttactaaattataataccctgtgctggcaaaggtgcagtgaaatgggcaccttcttatactatgaggggtgtttaaattgtgtataagccttccgggtaaagcCTGTCAATTTTTTAAAATAAtggagacagggtctcaccatactgccatactgcctcctccaactcttggcctcaagcaatcctcctctcttagcctcccaaagtgctaagattatagctgggaggcaccCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAACAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACttttttgttgttttgagacagggtctcactctgtcacccaggctggagtgcagaggcctgatcatgactcactgcagtctcagcctccctgggctcaagtgatcctcccacctcagcctcccaagtagctgggactacaggaacatgccaccacactaggctaattcatgtatttttctgtagggatggtgactccccctttgttccaaggcctatcgcaaactcttggcctcaagccatcctcctgcctcagcctcccaaagtgttgcgattaccagtgtgagccaccacacctggccAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCACAGCATAATTGTAAAAACATATagtcgtcgtcctcagtatacagaattagttccagccccccatctctgcatataccaaaatccatgcttactcacgtttgctgtcacccctctggaatccacgtatacgaaaattccaaatttagttgggcatagtggcaagcacctgtagtctcagccacgtgggaggttgaggtgggaggatcgcttcagcctggaaggttgaggctgcagtcagctgcgatagcactactacactccagccttggacaacagagggagaccctgtctcagaaaaaaaaaaaaataaaaCAGGTTAGAAACTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAAAGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGGCTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAAGACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCGGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTAATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTTTTTTTTAGAAAATTGAACAAGTGCTCCTgtggtggcacatgcctcgaggatgggaggcaggggtggaagggtcacttgaggccattagtttgacaccagcctggccaacaaagtgagaccccgtgtctacaaaacaatttaaaaattagccaagtatcatcatgtatacctacagtcccagctacCTGAACTTACTGAGAAAGTTCAGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCTCATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttccattattacactgtaatatataataaaataattatagaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggatgtcccacctgagcgtgatgggagaaagtaacagatcaataggtattagattctcataaggacagcgcaacctgatccctcacatgcacggttcacaacagggtgcgttctcctatgagaatctaacgctgctgctcatctgagaaggtggagctcaggcgggaatgtgagcaaaggggagtggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtgctccttgcggctccatggctcaggggttggggacccctgCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60  GT      ./.     ./.     ./.
chr1    814625  INS0005 T       <INS>   30      .       END=814625;SVTYPE=INS;SEQ=GGAAATGTTAATTCTGAAAATAGGTTTCACATCTTTTTTTTAACTTATATAAAATTGACTGGATTTCTCTTCTGTGTGTTGTGTTAGATATTTAGGA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.     ./.     ./.
chr1    831217  DEL0001 T       <DEL>   30      .       END=833736;SVTYPE=DEL;SEQ=TTGtcttatgtttaaaaatgtccttcagtcattgcaggtcacaagcaggctatcagctcagtaattaaaataattcggttcttcatagtgaatgtaattctaaattagattttaagttgtaactccctgcttcagcAATGGTGATGGGGCCTAGAAACCAGAGCACCTGAGCTCCATCCTACAGGGGGCCATACCGGGATCTTTCCATTTTCAGAGGCTTCTCTCTGACAGTGAAGTGTGATGACAGACTTGGGGGCAGGGCAATGGCTAGCTTCTGAAAGCCGCTGGCACTTTAGTGATAAATTTAAATTAAGTGACGGGTAGTGAGGTGTTTGTCAAGGAAAGTGCCGTCCAAATGCTAAATACTGATTATTTCTGCAGCAGTGACTGCAATACCTCACTCAATCTCTGTCTTTCTTGAAGAAGTCATAAATAAACACGATGAATCTATGTAGAAGCGGTAAGTCAGAAAAATCTGTGTGTTTCATTACATAAACAACGGTTTATCATTAATTGACAGGCTTGGATTGGGAGTTGTTAATGAAACTGATGAGATGTTGGACAGATGAGCTCCCTCTTATTTCGAAGAGCTTATCTAGGGCTGAGTCATGGGACCTGATAGCGTCTTGTGGTGCTGTCTTCTTGTAGATATATCCGTGTTTTAGAGGATTTAGTTTTTTAAAATTTCTCTTAGAATGTGAATTTTACAAAAAAGCACTTCCCAAATGGATGATTATTTGAAAAATGAATTGTCAGACAAAACTGACACATCAGTTATGGAGAAAACCCTTCAAGAACTGGCTTTAAATGTGTTTTAGTGGGAGCCACAGTGTGGAGAGAAACAGAAGAGGGAGGAGAGGGCGCCCCTTGTTTCTTCTCTCCACAGCCAGGCCTTCGCCACCTTTCTCAGTGTCTTCAAGAATAAAATGCCTCCGTTGTTGGTTTTAGCTGCTTTTCTCCCTCGGGGTAGGTAAAGTGGTTCCAAAACGACAAGCATCCTGTAAAGTCGGAAGAGCTGTGTCAACATTAAGCTGCGTGACTTTGGCTATGAGGGAAAAAAGGCTGGTGAGTGCAGAGAAGACAGAGCTGTGGCAGGGCTCCTCCCGCCAAGTCGCCATGGAGAGGGGCTGTGAGGTGTCCTTAAACGGCCTGGTCTCCAGGGTGACTCAGGAAGGGCTGAGAGTGGTCAGCTCCCTCACCTGCTAAACCCGCAGCGCCCCGCTCAGCACACACCCTCCACTCTCCAACCTTGCCCAAGTGCTGGTCCGTCACGGCACCAGGACAGGGCATGGAGACTTGGGCTGAttcttttctctcccttcctccctcttttttttcttctctcactcctccttttcctttcctgctgtttcctgctctcctgtttctGTCCTGCAGTGTCTGGAGCTCCAGAGAGGCTGGCCCTGGGGTGGGGTCCACATGGACATGGGCGTAAGCAGGTTTGATGGTCATGGGCATAGGCAGGTTCGATGGCCAGAGTTCTTTCAGCTCACAGTAAgttttgttttgttttgttttgttttgttttgttttgttttgttttagatggagtcttgctttgtcgcccaggctgtagtgcagtggcgtgatcttggctcactgcagcctccaccttagagcaatcctcttgcctcatcctcccgggtagttgggactacatgtgcatgccacatgcctggctaatttttgtatttttagtagagacacggtttcaccatgttggccaggctggtgtccaactcctgacctcaggtgatccatccgcctcagcctcccaaagtgccgggattacaggtatgagccactgcacctggccTCAGCTGACAGTAGGTTTTAGAGCCAGATATTTACACACTAACTTGCCAGAAACATATATGACTTTATTATTCTAATTGATTTTAAGAGATATTATGAACTCAAATCCAAAGTTACGTCCCACCTATCATGACAATTTCATTAAGGAAAAAGTCAAACCATTTTGGAAATGATTTAAGTGAGCAACTTGGAAAAATTTTCTACATTCCTAACTTACTTTCCAGGGGATCGTTCCTGACTTAACATCTATCAGGTGTCTTAGCTTAGCTCTCTTTTTACTTCAGGTTTTTCTTGCCTCCTCAGTGTGCTGGGAGTCCCACTCCACTCAAATGCCCTCAGGTCTAATAATTAACTTCATTGCAGGCTCCTGGCAGGCCTGGGTGGGCGGCAGCTGCATTGTGCTCCTGAAGAAGATTTAAGTTGGGTTTGGTGAACTGGTAGAATTTGCATTTTGCTGTTTCTTTCCCTCTCCCAGAATTTGTACCTTTAAATAGGTTTTTTAGTGTCATTAAGTATATCAAAAGGAAACCCAGTGGGGCAAATTGGCCGGGCTccatagaggtggccttgtctaagcctttcatcttatcgataaggaaagacaggaccagagaagtCGCCGACTGTCCCTGGTCCCACTGCTTGGTTTGGGGCAATTTCCTGAAAATAATATCCAAGATGCA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60   GT      ./.     ./.     ./.
chr1    1195963 INS0006 A       <INS>   30      .       END=1195963;SVTYPE=INS;SEQ=TGGGGTCTCACCATGTTGGCCAGGCTGgtctcaaactcctgagctcaagcgatcctcctgcctcagcctcccaaagtgctgggactacaggtgtgagccatgcgcccgaccaatttgtgtatttttagtagagatggggtctcaccatgttggccaggctggtctcaaactcctgagctcaagcgatcctcctgcctcagcctcccaaagtgctgggactacaggtgtgagccacgcgcctgaccAACTTGTGTATTTCTAGTAGAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60      GT      ./.     ./.     ./.
chr1    1240675 INS0007 C       <INS>   30      .       END=1240675;SVTYPE=INS;SEQ=CAGCcccccgcccccattcaccccggccgtggtccctgccccagcccccgccgcccccattcaccccggccgtggtccctgccc;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60     GT      ./.     ./.     ./.
chr1    1248055 DEL0002 A       <DEL>   30      .       END=1248319;SVTYPE=DEL;SEQ=GGCTGGATCTCCAACTCTGACCTACAGGCAGGAAAGTGGGCAGCCCTGGGAGGCTGGACTGAGGGAGGCTGGACTTCCCACTCAGGCCTACACGCAGGAAAATGGGCAGCCCTGGGAGGCTGGACCGAGGGAGGCTGGGCCTCCCACTCCACCCTACAGGCCAGGACACGGGCAGCCCTGGGAGGCTAGACCGAGGGAGGCTGGGCCTCCCATCTACCCTACAGGCCGGGACACAGGCAGCCCTGGGAGGCTGTACCGAGGGAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.     ./.     ./.
chr1    1477854 INS0008 C       <INS>   30      .       END=1477854;SVTYPE=INS;SEQ=CccaccacgcctggctaatgttgtattttagtagagacggggtttctccatgttggtcaggctggtctctaactcccgacctcaggtgatccacccgcctcggcctctcaaactgttgggattacaggcatgT;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60    GT      ./.     ./.     ./.
chr1    1494665 INS0009 A       <INS>   30      .       END=1494665;SVTYPE=INS;SEQ=TGGTGTGCTGCTGCCCCTGCACCCCGTGAGATGAATCCTGCCTCTGGGAGGTACAGCTTCCTGGAGGGGTGGCCCTGTGAGCATCTGCGTAGCCCCTCTCCTCTGCTGGGCCCTGGGTGACGTGCAGCCACTCGGGTGGACCCTGAGGGTCCCTGCACCTGTTTGCCCTCTCTTGGGTGGGCTCAAGACCAAAAATGATGTTGAGCAGTCCTGGGCCCCTGAGCCACAGTGGCGGTGCGGCTCCGGTCAGTGTCTCCTGCGCTCCCGGGCCCCCGACCCACAGTGGCGGTCCGGCTCTGGTCAGTGTCTCCTGCGCTCCCGGGCCCCCGACCCACAGTGGCGGTCCGGCTCCGGTCGGTGTCTCCCCACACAGTGGCTCTTGGCGAGGGGTGGGCGCTGGCAGAGGGGACGGGCACCACGTGGTCATCCCCATGACAGGTTCTGTCATGGTGACAGTGTTGTGGAGGA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60     GT      ./.     ./.     ./.
chr1    1565684 INS00010        T       <INS>   30      .       END=1565684;SVTYPE=INS;SEQ=GGTGCAGGCAGAGAACAGACGTCGCGATGGGCCCGACGGTGCTGGCTCCATGGGAACCGAGACCCAACACCCAAAGGAGTCCCACAGGCTCAGGGG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.     ./.     ./.

Lifted to GRCh37 will look like:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  GENOTYPE
chr1    59605   INS0000 C       <INS>   30      .       END=59605;SVTYPE=INS;SEQ=tttcttttttttttttttttttttttgaggagttccttgtcgccgctgggtggcggcgcgattgctcctgcagctccgcccccgtccccattcctgcctcgcctcccaagtactggactcagcgccccctcgcccggctaatttttgtatttttagtaagacgtttccgtttagcggggttcgatctctgacttcgtgtcctccgcctcgctcccagtgtgattacagCTGACCACCCCCCCAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60       GT      ./.
chr1    114350134       INS0001 A       <INS>   30      .       END=114350134;SVTYPE=INS;SEQ=TGTCTCTAGCACCTGGGATGGGCCTGATGTGTAACAGCTGCTGGCTGAACAGAAAGtgacagatgagcaaacatctcaaggaggtgatgaggatggtgatgagtgagaactcccgacatgtgaagataactgaagatgttctggctaaagatccgaagactctaagaatatgatcattccctttgaatatcaaatatcaaaagggctgtcaggtggagaagtgagtaaacttgtatcagaatagcggcagagTTGCAAGGAAACAGATCTCTGTTCTGTTAAAAAAAAAAAATTCCATAAACAACTGCATCACTTTGCATAGCAATTAGGTTCCAGCTCACAAGCGCCTTCCGGGGTGCCCCAAGGGTGAATCCTGCTAAGGTGGAGGTAGAAGACATGACCCTGGGGCTCTTTCCTTAGCCAAGAGCCCATGAGACTAAGGAACATCGTGCTTGTTGACAAAGACCCCGGACAGTCTATTCTCTTACGGTCACAGGCTATGGTGCCAAGGACAAGTGCAGACTCAGGATCAGAAAGCTTGCAGCATATCTGCTATCTCCATGGATAGCAGGATGGTCTGGAAGGCTGTGTCGGAAGGCCCTTAGGCCTCACTGGGGCCAGGCCGTTGATGAACAATGTCCACCCTGAGGGTCGGGAATGGTGCCATTTGTTTGTCATTCCTGGTCCAGACGCCCTTGGCTTGGTGGCTACTCAAGTAGGTCAGTTTACAAGCTCAGTGCTGAACCCATACCCTATGGCACGCTCGCCAGCACTAGAGAGGAAGCTGCCTCTGTGGACATCAGGGACGGAAGTGGCTCACCCAGCCTGTTCTGCGCGTGTCTCACTAAGGGTCCATCTTCCTCTATCTGCCCCGGAGGGGACCATCTCCAAGCATCCCTTGCTTTCCTTCTCCCCCCTCCACCCTCACTGTTCAATAACTTGAGTGCATCCCATTTGTAGAGCACATGCTGGGCCGTGGAGTGAAAGACAATCAGACGACACACATCCACATTCAAAGGGACTCAGGGCTCCTGGGAAGTAGAAATGAATATCAATAACCAAACATCCCacagcctgggtttcacatctgtttagcagcaggtgaccctggggaggtcactaactggtctctgcctcagcttcttccactgaaaaacaggaatggtcccttctacatcatggatactgtgaggTGAGAAGGAGCTGATCATGGCCCATCAACCTCAGCACACCAGTCCCCCTAGAGGCTGCTGGGAGAAGAAGCAGGGAGCACCCACTCCTGACCCAGATTCACATTCACTGCTCTCCTCCCCTGCCTCTGTCATGACCCCAGGGAAGCAGACGCTGAACCTGGGCTCTTGCCTTCATCTTTATCTTCTCCACTCTGGGATAATTAAGAATGACTTGCTAATTATGCAGATCTAGTGCAATGTGTAACTTCGGGCCACCAGTGCCAATCAGTAGAGCGGAGATGACGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaTCAAATCAATTTAAAAAACAATAAACTCCACCACCTCCCCCCTCACCCTCCCGTCATCTGCACTGATTTGTTCTCCCGGGAGCTGGAGAGGAGGGGGGGGGGGCAGCG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60        GT      ./.
chr1    645959  INS0002 T       <INS>   30      .       END=645959;SVTYPE=INS;SEQ=AAAGAACTGCCCGCCggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagatcgagaccatcccggctaaaacggtgaaacccgtctctactaaaaatacaaaaattagccgggcgtagtggcggcgcctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagccgagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaa;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60        GT      ./.
chr1    667757  INS0003 A       <INS>   30      .       END=667757;SVTYPE=INS;SEQ=GACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCAGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTACATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGCGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTCTTTTTTAGAAAATTGAACAAGTGCTCCCTGTGGTGGCACATACCTCGAGGAtgggaggcagggtggaagggtcacttgaggccattagtttgacaccagcctggccaacaaagtgagaccccgtgtctacaaacaatttaaaaattagccaagtatcgtcatgtatacctacagtcccagctaTCTGAACTTACTGAGAATGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGGCTCATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCTGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttgcattattacactgtaatatataataaaataattatagaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggatggtcccacctgagcgtgatgggagaaagtgacagatcaataggtattagattctcataaggacagcgcaacctagatccctcacatgcacggttcacaacagggtgcgttctcctatgagaatctaacgctgctgctcatctgagaaggtggagctcaggcgggaatgtgagcaaaggggagtggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtggctccttgcggctccatggctcaggggttggggacccctgCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAAGGGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCGGGAAACCAAACCTATGCCCAAATCCATCTGTGTGGGTGTATCTCCTGGGACCCTTCCTAACAtattagtcagagtccaatcaggaagcataaaccactcaaaagtttaaagtggtaaaatttaatacagagaattattcattgtaacaggtgaacagcataatgagagattggctagcacaaagtaaacagaactctagagaatataggactagcCCAggccaggcatggtggctcaggcctgaaattccagcaatttgagaagctaatgcaggaggattgcttaaggccaggagctagagaccggtctggacgacacagtgagaccctgtctctatccaaaagaagaaaaaagttagctgggggtggtagtgcacacttgtagtcccagctactcggaatgcggaagtttgagcctgggaggtcaaggctgcagtgaggcatgattatgccactacagtccagcctggtgacagagcaagaccctgtctcaaagaacaaaaCAACAACAACCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTgaaatgtgacaagtaaagtaatatgagttcttttgtctatgtaaaataatcaaacaaaaaatgacttactaaattataataccctgtgctggcaaaggtgcagtgaaatgggcaccttcttatactatgaggggtgtttaaattgtgtataagccttcccgggtaaagcctgtcaattttttaaaataatggagacagggtctcaccatactgccatactgcctcctccaactcttggcctcaagcaatcctcctctcttagcctcccaaagtgctaagattatagctgggaggcaccCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAACAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACttttttgttgttttgagacagggtctcactctgtcacccaggctggagtgcagaggcctgatcatgactcactgcagtctcagcctccctgggctcaagtgatcctcccacctcagcctcccaagtagctgggactacaggaacatgccaccacactaggctaattcatgtatttttctgtagggatggtgactccccctttgtttccaaggcctatcgcaaactcttggcctcaagccatcctcctgcctcagcctcccaaagtgttgcgattaccagtgtgagccaccacacctggccAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCCACAGCATAATTGTAAAAACATATAGTCgtcgtccctcagtatacagaattagttccagccccccatctctgcatataccaaaatccatgcttactcacgtttcgctgtcacccctctagaatccacgtatacgaaaattccaaatgttagttgggcatagtggcaagcacctgtagtctcagccacgtgggaggttgaggtgggaggatcgcttcagcctggaaggttgaggctgcagtcagctgcgatagcactactacactccagccttggacaacagagggagaccctgtctcagaaaaaaaacaaaataaaaCAGGTTAGAAATTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAAAGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGACTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60        GT      ./.
chr1    672482  INS0004 G       <INS>   30      .       END=672482;SVTYPE=INS;SEQ=GGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCATCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCGGGAAACCAAACCTATGCCCAAATCCCATCTGTGTGGGTGTATCTCCTGGGACCCTTCCTAACAtattagtcagagtccaatcaggaagcataaaccactcaaaagtttaaagtggtaaaatttaatacagagaattattcattataacaggtgaacagcataatgagagattggctagcacaaagtaaacagaactctagagaatatggactagcCCAggccaggcatggtggctcagcctgaaattccagcaatttgagaagctaatgcaggaggattgcttaaggccaggagctagagaccggtctggacgacacagtgagaccctgtctctatccaaaagaagaaaaaagttagctgggggtggtagtgcacacttgtagtcccagctactcggaatgcgaagtttgagcctgggaggtcaaggctgcagtgaggcatgattatgccactacagtccagcctggtgacagagcaagacctgtctcaaagaacaaaacaacaacaaCCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTgaaatgtgacaagtaaagtaatatgagttcttttgtctatgtaaaataatcaaacaaaaaatgacttactaaattataataccctgtgctggcaaaggtgcagtgaaatgggcaccttcttatactatgaggggtgtttaaattgtgtataagccttccgggtaaagcCTGTCAATTTTTTAAAATAAtggagacagggtctcaccatactgccatactgcctcctccaactcttggcctcaagcaatcctcctctcttagcctcccaaagtgctaagattatagctgggaggcaccCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAACAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACttttttgttgttttgagacagggtctcactctgtcacccaggctggagtgcagaggcctgatcatgactcactgcagtctcagcctccctgggctcaagtgatcctcccacctcagcctcccaagtagctgggactacaggaacatgccaccacactaggctaattcatgtatttttctgtagggatggtgactccccctttgttccaaggcctatcgcaaactcttggcctcaagccatcctcctgcctcagcctcccaaagtgttgcgattaccagtgtgagccaccacacctggccAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCACAGCATAATTGTAAAAACATATagtcgtcgtcctcagtatacagaattagttccagccccccatctctgcatataccaaaatccatgcttactcacgtttgctgtcacccctctggaatccacgtatacgaaaattccaaatttagttgggcatagtggcaagcacctgtagtctcagccacgtgggaggttgaggtgggaggatcgcttcagcctggaaggttgaggctgcagtcagctgcgatagcactactacactccagccttggacaacagagggagaccctgtctcagaaaaaaaaaaaaataaaaCAGGTTAGAAACTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAAAGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGGCTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAAGACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCGGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTAATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTTTTTTTTAGAAAATTGAACAAGTGCTCCTgtggtggcacatgcctcgaggatgggaggcaggggtggaagggtcacttgaggccattagtttgacaccagcctggccaacaaagtgagaccccgtgtctacaaaacaatttaaaaattagccaagtatcatcatgtatacctacagtcccagctacCTGAACTTACTGAGAAAGTTCAGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCTCATCTGCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAgatgtaagcacatttgcatttattaggcactttatttccattattacactgtaatatataataaaataattatagaactcaccataatgtagaatcagtgggcgtgttaagcttgttttcctgcaactggatgtcccacctgagcgtgatgggagaaagtaacagatcaataggtattagattctcataaggacagcgcaacctgatccctcacatgcacggttcacaacagggtgcgttctcctatgagaatctaacgctgctgctcatctgagaaggtggagctcaggcgggaatgtgagcaaaggggagtggctgtaaatacagacgaagcttccctcactccctcactcgacaccgctcacctcctgctgtgtgctccttgcggctccatggctcaggggttggggacccctgCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60  GT      ./.
chr1    750005  INS0005 T       <INS>   30      .       END=750005;SVTYPE=INS;SEQ=GGAAATGTTAATTCTGAAAATAGGTTTCACATCTTTTTTTTAACTTATATAAAATTGACTGGATTTCTCTTCTGTGTGTTGTGTTAGATATTTAGGA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.
chr1    766597  DEL0001 T       <DEL>   30      .       END=769116;SVTYPE=DEL;SEQ=TTGtcttatgtttaaaaatgtccttcagtcattgcaggtcacaagcaggctatcagctcagtaattaaaataattcggttcttcatagtgaatgtaattctaaattagattttaagttgtaactccctgcttcagcAATGGTGATGGGGCCTAGAAACCAGAGCACCTGAGCTCCATCCTACAGGGGGCCATACCGGGATCTTTCCATTTTCAGAGGCTTCTCTCTGACAGTGAAGTGTGATGACAGACTTGGGGGCAGGGCAATGGCTAGCTTCTGAAAGCCGCTGGCACTTTAGTGATAAATTTAAATTAAGTGACGGGTAGTGAGGTGTTTGTCAAGGAAAGTGCCGTCCAAATGCTAAATACTGATTATTTCTGCAGCAGTGACTGCAATACCTCACTCAATCTCTGTCTTTCTTGAAGAAGTCATAAATAAACACGATGAATCTATGTAGAAGCGGTAAGTCAGAAAAATCTGTGTGTTTCATTACATAAACAACGGTTTATCATTAATTGACAGGCTTGGATTGGGAGTTGTTAATGAAACTGATGAGATGTTGGACAGATGAGCTCCCTCTTATTTCGAAGAGCTTATCTAGGGCTGAGTCATGGGACCTGATAGCGTCTTGTGGTGCTGTCTTCTTGTAGATATATCCGTGTTTTAGAGGATTTAGTTTTTTAAAATTTCTCTTAGAATGTGAATTTTACAAAAAAGCACTTCCCAAATGGATGATTATTTGAAAAATGAATTGTCAGACAAAACTGACACATCAGTTATGGAGAAAACCCTTCAAGAACTGGCTTTAAATGTGTTTTAGTGGGAGCCACAGTGTGGAGAGAAACAGAAGAGGGAGGAGAGGGCGCCCCTTGTTTCTTCTCTCCACAGCCAGGCCTTCGCCACCTTTCTCAGTGTCTTCAAGAATAAAATGCCTCCGTTGTTGGTTTTAGCTGCTTTTCTCCCTCGGGGTAGGTAAAGTGGTTCCAAAACGACAAGCATCCTGTAAAGTCGGAAGAGCTGTGTCAACATTAAGCTGCGTGACTTTGGCTATGAGGGAAAAAAGGCTGGTGAGTGCAGAGAAGACAGAGCTGTGGCAGGGCTCCTCCCGCCAAGTCGCCATGGAGAGGGGCTGTGAGGTGTCCTTAAACGGCCTGGTCTCCAGGGTGACTCAGGAAGGGCTGAGAGTGGTCAGCTCCCTCACCTGCTAAACCCGCAGCGCCCCGCTCAGCACACACCCTCCACTCTCCAACCTTGCCCAAGTGCTGGTCCGTCACGGCACCAGGACAGGGCATGGAGACTTGGGCTGAttcttttctctcccttcctccctcttttttttcttctctcactcctccttttcctttcctgctgtttcctgctctcctgtttctGTCCTGCAGTGTCTGGAGCTCCAGAGAGGCTGGCCCTGGGGTGGGGTCCACATGGACATGGGCGTAAGCAGGTTTGATGGTCATGGGCATAGGCAGGTTCGATGGCCAGAGTTCTTTCAGCTCACAGTAAgttttgttttgttttgttttgttttgttttgttttgttttgttttagatggagtcttgctttgtcgcccaggctgtagtgcagtggcgtgatcttggctcactgcagcctccaccttagagcaatcctcttgcctcatcctcccgggtagttgggactacatgtgcatgccacatgcctggctaatttttgtatttttagtagagacacggtttcaccatgttggccaggctggtgtccaactcctgacctcaggtgatccatccgcctcagcctcccaaagtgccgggattacaggtatgagccactgcacctggccTCAGCTGACAGTAGGTTTTAGAGCCAGATATTTACACACTAACTTGCCAGAAACATATATGACTTTATTATTCTAATTGATTTTAAGAGATATTATGAACTCAAATCCAAAGTTACGTCCCACCTATCATGACAATTTCATTAAGGAAAAAGTCAAACCATTTTGGAAATGATTTAAGTGAGCAACTTGGAAAAATTTTCTACATTCCTAACTTACTTTCCAGGGGATCGTTCCTGACTTAACATCTATCAGGTGTCTTAGCTTAGCTCTCTTTTTACTTCAGGTTTTTCTTGCCTCCTCAGTGTGCTGGGAGTCCCACTCCACTCAAATGCCCTCAGGTCTAATAATTAACTTCATTGCAGGCTCCTGGCAGGCCTGGGTGGGCGGCAGCTGCATTGTGCTCCTGAAGAAGATTTAAGTTGGGTTTGGTGAACTGGTAGAATTTGCATTTTGCTGTTTCTTTCCCTCTCCCAGAATTTGTACCTTTAAATAGGTTTTTTAGTGTCATTAAGTATATCAAAAGGAAACCCAGTGGGGCAAATTGGCCGGGCTccatagaggtggccttgtctaagcctttcatcttatcgataaggaaagacaggaccagagaagtCGCCGACTGTCCCTGGTCCCACTGCTTGGTTTGGGGCAATTTCCTGAAAATAATATCCAAGATGCA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60   GT      ./.
chr1    1131343 INS0006 A       <INS>   30      .       END=1131343;SVTYPE=INS;SEQ=TGGGGTCTCACCATGTTGGCCAGGCTGgtctcaaactcctgagctcaagcgatcctcctgcctcagcctcccaaagtgctgggactacaggtgtgagccatgcgcccgaccaatttgtgtatttttagtagagatggggtctcaccatgttggccaggctggtctcaaactcctgagctcaagcgatcctcctgcctcagcctcccaaagtgctgggactacaggtgtgagccacgcgcctgaccAACTTGTGTATTTCTAGTAGAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60      GT      ./.
chr1    1176055 INS0007 C       <INS>   30      .       END=1176055;SVTYPE=INS;SEQ=CAGCcccccgcccccattcaccccggccgtggtccctgccccagcccccgccgcccccattcaccccggccgtggtccctgccc;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60     GT      ./.
chr1    1183435 DEL0002 A       <DEL>   30      .       END=1183699;SVTYPE=DEL;SEQ=GGCTGGATCTCCAACTCTGACCTACAGGCAGGAAAGTGGGCAGCCCTGGGAGGCTGGACTGAGGGAGGCTGGACTTCCCACTCAGGCCTACACGCAGGAAAATGGGCAGCCCTGGGAGGCTGGACCGAGGGAGGCTGGGCCTCCCACTCCACCCTACAGGCCAGGACACGGGCAGCCCTGGGAGGCTAGACCGAGGGAGGCTGGGCCTCCCATCTACCCTACAGGCCGGGACACAGGCAGCCCTGGGAGGCTGTACCGAGGGAG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.
chr1    1413234 INS0008 C       <INS>   30      .       END=1413234;SVTYPE=INS;SEQ=CccaccacgcctggctaatgttgtattttagtagagacggggtttctccatgttggtcaggctggtctctaactcccgacctcaggtgatccacccgcctcggcctctcaaactgttgggattacaggcatgT;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60    GT      ./.
chr1    1430045 INS0009 A       <INS>   30      .       END=1430045;SVTYPE=INS;SEQ=TGGTGTGCTGCTGCCCCTGCACCCCGTGAGATGAATCCTGCCTCTGGGAGGTACAGCTTCCTGGAGGGGTGGCCCTGTGAGCATCTGCGTAGCCCCTCTCCTCTGCTGGGCCCTGGGTGACGTGCAGCCACTCGGGTGGACCCTGAGGGTCCCTGCACCTGTTTGCCCTCTCTTGGGTGGGCTCAAGACCAAAAATGATGTTGAGCAGTCCTGGGCCCCTGAGCCACAGTGGCGGTGCGGCTCCGGTCAGTGTCTCCTGCGCTCCCGGGCCCCCGACCCACAGTGGCGGTCCGGCTCTGGTCAGTGTCTCCTGCGCTCCCGGGCCCCCGACCCACAGTGGCGGTCCGGCTCCGGTCGGTGTCTCCCCACACAGTGGCTCTTGGCGAGGGGTGGGCGCTGGCAGAGGGGACGGGCACCACGTGGTCATCCCCATGACAGGTTCTGTCATGGTGACAGTGTTGTGGAGGA;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60     GT      ./.
chr1    1501064 INS00010        T       <INS>   30      .       END=1501064;SVTYPE=INS;SEQ=GGTGCAGGCAGAGAACAGACGTCGCGATGGGCCCGACGGTGCTGGCTCCATGGGAACCGAGACCCAACACCCAAAGGAGTCCCACAGGCTCAGGGG;CIPOS=-10,10;CIEND=-10,10;IMPRECISE;MAPQ=60 GT      ./.

The error isn't really helpful. What am I doing wrong?

traxexx commented 3 years ago

Here is the message: chr1:114350134 Padding base in genome is different from VCF. Use the one from genome This indicates that the base at this position in your vcf is different from the base from your reference fasta. There could be 2 possibilities:

  1. Are you using GRCh37 as the reference fasta to Paragraph, when you use the lifted vcf?
  2. The lifted vcf could be wrong.

Could you please double-check these two things?

Parsoa commented 3 years ago

The problem was actually that my BAM file was mapped against a reference that didn't have "chr" prefix for chromosomes, while my VCF and FASTA file had those prefixes.