ekg
commented
4 years ago Note that vg map will write BAM directly. Try running a few reads that way and see if they are still unmapped.
On Fri, Dec 20, 2019, 09:41 Kübra NARCI notifications@github.com wrote:
I want to use VG map alignment file to use with GATK4 haplotypecaller. In order to do that I used the instructions mentioned here ( https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph) to work through whole-genome. Then I converted (sorted) GAM file to BAM file using VG surject (to bam option). Yet, in sorted and indexed BAM file, ALL reads seems to be unmapped (mostly flag 4). Do you have any idea on what I am missing though the process?
Mostly like this: HISEQ1:22:H9UJNADXX:2:1106:20572:14228/1 4 0 0 0 0 AGTTGGCAGAGAAGGCCTCTTGTGCTCACGCTCCCCCGCAGTCCCCAGCCCTTCTGCCTTTCTCCCCCGACACTGCTGCACCAGAGTGAAAGGGCTATGGCAAGGGGGTGTCATCTGAGGAGTATTAAGAATGCAGATTCCTGGGCCT @@@FFFFFHHHHGJIIJIJFIJEHIGIJIJJJJIJJIHIJIIJJIJIEIJH@HGFFFFEFEEEDEDDDBDDBBCDCDDDDDDDDDDCCCACDDDD ?BDDDBDDBBBDB5>BCCDDDC>CBA@9?CDDEDDDDDDACDCCDDDDDDBB@ HISEQ1:22:H9UJNADXX:2:2212:3639:78995/1 4 0 0 0 0 TTCCCAGCTCACCATCAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCCCTGGGGACAAAAGGAGCTGGGTACAGGGGTTGCTCTAGCAGGCACAGCACAGACCCCGGAGA CCCFFFFFHHHHHJJJJJJJJJJJJJJGJJJJJJIJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJHHFFFDDDDDDDDDDDDDDDDDDDDDDDDDDBBDDDD?CDDEDDDBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB HISEQ1:22:H9UJNADXX:2:2212:3639:78995/1 4 0 0 0 0 TTCCCAGCTCACCATCAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCCCTGGGGACAAAAGGAGCTGGGTACAGGGGTTGCTCTAGCAGGCACAGCACAGACCCCGGAGA CCCFFFFFHHHHHJJJJJJJJJJJJJJGJJJJJJIJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJHHFFFDDDDDDDDDDDDDDDDDDDDDDDDDDBBDDDD?CDDEDDDBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB HISEQ1:22:H9UJNADXX:1:2204:1672:85287/1 4 0 0 0 0 CAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCACTGGGGACAAAAGGAGCTGGGTACAGGGATTGCTCTAGCAGGGACAGCACAGACCCCGGAGAAAGCCCACAACAATA CCCFFFFFHHHHHJJJJJGGHIJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJIJJHFHFDDD';?CDDDBDDDDDDDDDDDDDDCCDDEDD(+3<CDDDDDDDDB)2<BDDDDDDDDDDDDBDD@BDDDDDDDDDDDDDC HISEQ1:22:H9UJNADXX:1:2204:1672:85287/1 4 0 0 * 0 0 CAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCACTGGGGACAAAAGGAGCTGGGTACAGGGATTGCTCTAGCAGGGACAGCACAGACCCCGGAGAAAGCCCACAACAATA CCCFFFFFHHHHHJJJJJGGHIJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJIJJHFHFDDD';?CDDDBDDDDDDDDDDDDDDCCDDEDD(+3<CDDDDDDDDB)2<BDDDDDDDDDDDDBDD@BDDDDDDDDDDDDDC
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kubranarci
I want to use VG map alignment file to use with GATK4 haplotypecaller. In order to do that I used the instructions mentioned here (https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph) to work through whole-genome. Then I converted (sorted) GAM file to BAM file using VG surject (to bam option). Yet, in sorted and indexed BAM file, ALL reads seems to be unmapped (mostly flag 4). Do you have any idea on what I am missing though the process?
Mostly like this: HISEQ1:22:H9UJNADXX:2:1106:20572:14228/1 4 0 0 0 0 AGTTGGCAGAGAAGGCCTCTTGTGCTCACGCTCCCCCGCAGTCCCCAGCCCTTCTGCCTTTCTCCCCCGACACTGCTGCACCAGAGTGAAAGGGCTATGGCAAGGGGGTGTCATCTGAGGAGTATTAAGAATGCAGATTCCTGGGCCT @@@FFFFFHHHHGJIIJIJFIJEHIGIJIJJJJIJJIHIJIIJJIJIEIJH@HGFFFFEFEEEDEDDDBDDBBCDCDDDDDDDDDDCCCACDDDD?BDDDBDDBBBDB5>BCCDDDC>CBA@9?CDDEDDDDDDACDCCDDDDDDBB@ HISEQ1:22:H9UJNADXX:2:2212:3639:78995/1 4 0 0 0 0 TTCCCAGCTCACCATCAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCCCTGGGGACAAAAGGAGCTGGGTACAGGGGTTGCTCTAGCAGGCACAGCACAGACCCCGGAGA CCCFFFFFHHHHHJJJJJJJJJJJJJJGJJJJJJIJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJHHFFFDDDDDDDDDDDDDDDDDDDDDDDDDDBBDDDD?CDDEDDDBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB HISEQ1:22:H9UJNADXX:2:2212:3639:78995/1 4 0 0 0 0 TTCCCAGCTCACCATCAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCCCTGGGGACAAAAGGAGCTGGGTACAGGGGTTGCTCTAGCAGGCACAGCACAGACCCCGGAGA CCCFFFFFHHHHHJJJJJJJJJJJJJJGJJJJJJIJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJHHFFFDDDDDDDDDDDDDDDDDDDDDDDDDDBBDDDD?CDDEDDDBBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDB HISEQ1:22:H9UJNADXX:1:2204:1672:85287/1 4 0 0 0 0 CAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCACTGGGGACAAAAGGAGCTGGGTACAGGGATTGCTCTAGCAGGGACAGCACAGACCCCGGAGAAAGCCCACAACAATA CCCFFFFFHHHHHJJJJJGGHIJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJIJJHFHFDDD';?CDDDBDDDDDDDDDDDDDDCCDDEDD(+3<CDDDDDDDDB)2<BDDDDDDDDDDDDBDD@BDDDDDDDDDDDDDC HISEQ1:22:H9UJNADXX:1:2204:1672:85287/1 4 0 0 * 0 0 CAGATCTATTCTGAGCTTGTGCATTTGGCCTAGGCAAGACTGGCTGGCTGCTTGGGGCAGAGGGAGGGGCACTGGGGACAAAAGGAGCTGGGTACAGGGATTGCTCTAGCAGGGACAGCACAGACCCCGGAGAAAGCCCACAACAATA CCCFFFFFHHHHHJJJJJGGHIJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJIJJHFHFDDD';?CDDDBDDDDDDDDDDDDDDCCDDEDD(+3<CDDDDDDDDB)2<BDDDDDDDDDDDDBDD@BDDDDDDDDDDDDDC