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lindenb / jvarkit

Java utilities for Bioinformatics
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vcf2bam #86

Closed tcosta-f closed 7 years ago

tcosta-f commented 7 years ago

Subject of the issue

It doesn't accept the reference genome, it is indexed with samtools as well as Picard. I'm using it just fine in several software except in this tool. Also, I tried with different versions of samtools and Picard without success, same error!

Steps to reproduce

Tell us how to reproduce this issue. Please provide an example. ` $ '.../Downloads/jvarkit/dist/vcf2bam' -R '..../SNPs/fa/longest_uces_semZ.fa' '..../No_OUT/1SNPlocus_Pheugopedius-only-PASS-Q30-SNPs_maf0.014925373.vcf.gz' 2> '..../No_OUT/1SNPlocus_Pheugopedius-only-PASS-Q30-SNPs_maf0.014925373.bam' | grep -v "100="

`[SEVERE][VcfToBam]No REF defined [INFO][Launcher]vcf2bam Exited with failure (-1)

My files, vcf and ref 1SNPlocus_Pheugopedius-only-PASS-Q30-SNPs_maf0.014925373.vcf.gz longest_uces_semZ.fa.zip

Can you help me please?

Thanks

TSN

lindenb commented 7 years ago

ah yes, I can see the same bug. I have not used this program for years. Give me a few minutes...

lindenb commented 7 years ago

I've updated the code (I didn't test the program after I've added a line) Can you please update the code and try again ?

tcosta-f commented 7 years ago

Thank you, is running

But, now I'm getting this:

[SEVERE][VcfToBam]Variants are not ordered on sequence dictionary ([VC Unknown @ ACAexon1PhgSARMA101:117 Q230.02 of type=SNP alleles=[C*, T] attr={} GT=GT:AD:DP:GQ:PL 0/0:14,0:14:36:0,36,495 0/0:19,0:19:54:0,54,763 0/0:14,0:14:36:0,36,5100/0:14,0:14:42:0,42,582 0/0:21,0:21:57:0,57,774 0/0:10,0:10:27:0,27,383 0/0:15,0:15:45:0,45,614 0/0:34,0:34:66:0,66,924 0/0:47,0:47:99:0,111,1496 0/0:30,0:30:69:0,69,950 0/0:19,0:19:39:0,39,546 0/0:17,0:17:36:0,36,504 0/0:5,0:5:15:0,15,194 0/0:22,0:22:54:0,54,733 0/0:29,0:29:57:0,57,794 0/1:4,6:10:99:148,0,1040/1:7,5:12:99:138,0,172 0/0:16,0:16:36:0,36,477 0/0:31,0:31:75:0,75,999 0/0:21,0:21:48:0,48,652 0/0:30,0:30:72:0,72,978 0/0:3,0:3:6:0,6,76 0/0:32,0:33:75:0,75,1009 0/0:16,0:16:39:0,39,531 0/0:26,0:26:57:0,57,790 0/0:27,0:27:54:0,54,755 0/0:22,0:22:48:0,48,657 0/0:13,0:13:36:0,36,487 0/0:12,0:12:36:0,36,5050/0:10,0:10:27:0,27,378 0/0:10,0:10:27:0,27,383 0/0:20,0:20:45:0,45,608 0/0:18,0:18:39:0,39,544 0/0:17,0:17:33:0,33,469 0/0:31,0:31:66:0,66,923 0/0:14,0:14:27:0,27,384 0/0:26,0:26:60:0,60,809 0/0:47,0:48:99:0,105,1428 0/0:42,0:42:87:0,87,1214 0/0:33,0:33:75:0,75,1021 0/0:38,0:38:90:0,90,1223 0/0:14,0:14:36:0,36,473 0/0:52,0:52:99:0,102,1417 0/0:3,0:3:9:0,9,120 0/0:24,0:24:57:0,57,781 0/0:39,0:39:75:0,75,1048 0/0:23,0:23:51:0,51,7000/0:30,0:30:60:0,60,837 0/0:15,0:15:42:0,42,571 0/0:14,0:14:39:0,39,539 0/0:80,0:80:99:0,160,2217 0/0:24,0:24:48:0,48,669 0/0:28,0:28:63:0,63,870 0/0:32,0:32:78:0,78,1040 0/0:26,0:26:60:0,60,800 0/0:31,0:31:69:0,69,952 0/0:28,0:28:66:0,66,901 0/0:33,0:33:72:0,72,971 0/0:21,0:21:42:0,42,593 0/0:28,0:28:69:0,69,936 0/0:29,0:29:60:0,60,825 0/0:21,0:21:48:0,48,652 0/0:22,0:22:51:0,51,6950/0:19,0:19:39:0,39,546 0/0:27,0:27:60:0,60,811) java.io.IOException: Variants are not ordered on sequence dictionary ([VC Unknown @ ACAexon1PhgSARMA101:117 Q230.02 of type=SNP alleles=[C*, T] attr={} GT=GT:AD:DP:GQ:PL 0/0:14,0:14:36:0,36,495 0/0:19,0:19:54:0,54,763 0/0:14,0:14:36:0,36,510 0/0:14,0:14:42:0,42,582 0/0:21,0:21:57:0,57,774 0/0:10,0:10:27:0,27,3830/0:15,0:15:45:0,45,614 0/0:34,0:34:66:0,66,924 0/0:47,0:47:99:0,111,1496 0/0:30,0:30:69:0,69,950 0/0:19,0:19:39:0,39,546 0/0:17,0:17:36:0,36,504 0/0:5,0:5:15:0,15,194 0/0:22,0:22:54:0,54,733 0/0:29,0:29:57:0,57,794 0/1:4,6:10:99:148,0,104 0/1:7,5:12:99:138,0,172 0/0:16,0:16:36:0,36,477 0/0:31,0:31:75:0,75,9990/0:21,0:21:48:0,48,652 0/0:30,0:30:72:0,72,978 0/0:3,0:3:6:0,6,76 0/0:32,0:33:75:0,75,1009 0/0:16,0:16:39:0,39,531 0/0:26,0:26:57:0,57,790 0/0:27,0:27:54:0,54,755 0/0:22,0:22:48:0,48,657 0/0:13,0:13:36:0,36,487 0/0:12,0:12:36:0,36,505 0/0:10,0:10:27:0,27,378 0/0:10,0:10:27:0,27,383 0/0:20,0:20:45:0,45,6080/0:18,0:18:39:0,39,544 0/0:17,0:17:33:0,33,469 0/0:31,0:31:66:0,66,923 0/0:14,0:14:27:0,27,384 0/0:26,0:26:60:0,60,809 0/0:47,0:48:99:0,105,1428 0/0:42,0:42:87:0,87,1214 0/0:33,0:33:75:0,75,1021 0/0:38,0:38:90:0,90,12230/0:14,0:14:36:0,36,473 0/0:52,0:52:99:0,102,1417 0/0:3,0:3:9:0,9,120 0/0:24,0:24:57:0,57,781 0/0:39,0:39:75:0,75,1048 0/0:23,0:23:51:0,51,7000/0:30,0:30:60:0,60,837 0/0:15,0:15:42:0,42,571 0/0:14,0:14:39:0,39,539 0/0:80,0:80:99:0,160,2217 0/0:24,0:24:48:0,48,669 0/0:28,0:28:63:0,63,870 0/0:32,0:32:78:0,78,1040 0/0:26,0:26:60:0,60,800 0/0:31,0:31:69:0,69,952 0/0:28,0:28:66:0,66,901 0/0:33,0:33:72:0,72,971 0/0:21,0:21:42:0,42,593 0/0:28,0:28:69:0,69,936 0/0:29,0:29:60:0,60,825 0/0:21,0:21:48:0,48,652 0/0:22,0:22:51:0,51,6950/0:19,0:19:39:0,39,546 0/0:27,0:27:60:0,60,811) at com.github.lindenb.jvarkit.tools.misc.VcfToBam.run(VcfToBam.java:189) at com.github.lindenb.jvarkit.tools.misc.VcfToBam.doWork(VcfToBam.java:396) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:1155) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:1341) at com.github.lindenb.jvarkit.tools.misc.VcfToBam.main(VcfToBam.java:414) [INFO][Launcher]vcf2bam Exited with failure (-1)

I tried to reorder the vcf file using SortVcf (picard) but the error persists

What should I do?

lindenb commented 7 years ago

can you please show me the output of

cut -f 1 your.ref.fa

and the output of 

grep -v "#" your.vcf | cut -f 1 | uniq
tcosta-f commented 7 years ago

cut -f 1 your.ref.fa

ACAexon1PhgSARMA101 GCAGCAGCAGCAGCAGCAGCAGCATGGACATTACCATCCAGCACCCCTGGTTCAAGCGTGCCCTGGGACCCCTCATTCCAAGCCGTTTGTTCGACCAGTTTTTTGGAGAGGGTCTCCTCGAGTATGACCTCCTGCCTTTGTTCTCGTCCACTATCAGCCCCTACTACAGGCAGTCCCTCTTCCGCAGCGTGCTGGAGTCAGGCATTTCAGAGGTAAGGGCCCTTTGATTTCCTCTCCCTTCCCTTCCTCTCCCTCCTGATGCCTCCAGCCGCTCCTCTGCACCCACATCTCACACTGGTGTAGCCCCGT ACAexon2PhgMPDS1153 GTCCCTGGGTCCCCACAATGGGAAGAAGAGCCCTGCTGAGGCCCATAGTCACAGAAGGACAAAGTGCCAGACCACCCCATTTTTGGCCTTTAATCTGTGGTGGTGCTGGCACTGCCTCCACACGGGCCTCACTGTGTGACAATGCTCCTTTCAGGTGAGGTCCGATCGGGACAAGTTCACAATCATGCTGGATGTAAAACACTTCTCTCCTGAAGACTTGAGTGTGAAGATTATTGATGACTTTGTGGAAATCCATGGCAAGCACAGTGAAAGGCAGGTAAGTGGAAGTGATGGTGATGGTGGAGCAGCTGGGGAGTCCAGCTCCGTTTCCCTTCTTTCCAACGGTTCTCAGCTGAAGGAAAAAAAAAAGAATATATCAGAAGAAGGAGTTAATTATGAATTGTCATTATTGGCATGGCCTGTTCCCATAGAGCCCCCACCTGATATCTGACAATAACAA ARNTLexon12PhgAMANA102 TGTGCCAAACACTGATTATCTTCAACTTGCATGGGTTTGTAGGGAACATTTGAGGTTCAGGATGGGTGAGGGAGGAATAGCATTTTTCTTGAGGGATGTGGGGAGGGATTAACTGGGTTTTCCCTGACAAGGGCTCTGTTGATGTTGTGGTGCCTGCTTGACACGAATGACTTGCTTTCTGCCTGTTTTCAGTTTTGCAGACAAGAGAAAAAATTACAACTAACTGCTACAAGTTTAAAATAAAAGATGGCTCTTTTATTACGTTGCGGAGTCGCTGGTTCAGTTTCATGAACCCTTGGACCAAAGAAGTAGAATACATTGTCTCCACAAACACCGTGGTTTCGTAAGTGCCTGGGAATGCCCAGTGCTTTGCCCTTTTCTCATGGCATGAGATTTGACCTAAATATGTGCACACCTTCTGTATGACAGTAGGTGTCTTCTCCAGATAACACCCCAGGGAGAGGAGCTTTAGTTTAACAATTGCAGTAATTTAATTTCTGGTTGTTAAACCTTGAAGGAAATAGAAATATTTTCTTTCTT ARNTLexon13PhgGUR235 CACTGCAACCCATGACATAGGGTTTTCTCTCACTGATTTTCCTAATCCTTGCACTCCACAGCACCACGGTCCTGGACAGTGGGGACACGGCCTTTCCCCAGCTGGCAGCGTCCCCACACAGCATGGACAGCGTGCTCCAGGCTGGAGAAGGTAACTCCTGTGCTCAGGGAATCACTGGCTGCTGTGCCTTGGGAGCAGCTCACCCTGCCTGCACACATTGGCTGCCCTTCTGCACTGAGATG BDNFexonPhgAMANA102 TGGTTTTAACAGTTCCACCAAGTGAGAAGAGTGATGACCATCCTTTTCTTTACTATGGTTATCTCATACTTCACTTGCATGAAAGCTGCCCCGATGAAAGAAGCTAGTCTAAGAGCACAAGGCAGCTTGGCTTACCCAGGTCTTCGGACCCACGGGACTCTTGAGAGCATAAATGGGCCCAATGCTGGTTCAAGAGGACTGACATCATTGGCAGATACTTTTGAACATGTCATAGAGGAGCTTCTAGACGAGGACCAGGACATCCAGCCCAGTGAGGGAAACAAGGATGCAGACTTGTATACATCCCGAGTCATGCTAAGCAGTCAAGTGCCTTTGGAACCCCCACTGCTCTTTCTGCTTGAGGAATACAAAAACTACTTGGATGCTGCAAACATGTCCATGAGAGTCCGGCGCCACTCTGATCCAGCTCGCCGTGGGGAACTGAGCGTGTGTGACAGCACGAGCGAGTGGGTGACAGCAGCAGAGAAAAAGACTGCAGTGGACATGTCTGGGGCAACTGTCACAGTCCTGGAGAAAGTTCCAGTACCCAAAGGCCAACTGAAGCAATACTTCTATGAGACCAAATGCAACCCTAAGGGGTACACGAAGGAGGGCTGCAGGGGCATTGACAAGAGGCACTGGAACTCACAGTGCCGAACTACCCAGTCTTACGTGAGAGCTCTCACCATGGATAATAAAAAGAGAGTTGGCTGGCGCTTTATAAGGATAGACACTTCCTGTGTATGTACATTAACCATTAAAAGGGGAAGATAGTGGGTTCATGTTGTATAGATTATATTGAGACAAATATCTATTTGTATATATACATAACAGGGTAAATTATTCGGTAAAAAATAATTTTATGGACTGCATGTATG CALB1exon11PhgMPDS1153 CACATGGCCATCATATGGATGCCATACAAATATATAAAAACATTTTAGTGTGTTACTGTCAGACAGGCTGAGAATACCTGGGATTTTTTTCTCATTTCCTGCCATTGGAAGTAAACTTGTTCATGCTGATAACTAAACAGGATTATAAAGCCTTATCTGTTCTTTAAATAGGAATTAGACATTACCAACCTTGCAACATACAAGAAAAGCATCATGGCCTTGTCTGATGGAGGAAAGCTTTACCGAGCAGAACTGGCTCTTATTCTCTGTGCTGAGGAAAACTAGAGCTCTTCTATCATGTCCACTTAACTAGTGATGTACTCTACACAATAACTGTGCACTATAAGGGAGTAGGCTGTATTTTTAAACTGCATATAGAAAATTAGCCAGGATGTGTGGCACATTCCTTTCAGTTTGTTTCTATACTGTTTGTAATGTACAGTTTTTGTAACAATAA CHCexon4PhgAMANA102 AAGCAGCATTCAAAAGTAGCATGTTCTTATCTGTGGAGGAAATATCCATATATTTTAACTGCTTTTCAAGCTCTTCATTCTGCTGTGATAGTACTGAAGTAAAAATAAAACAGCACTTCTGGCTGTCCTGAAATGGCCCAGCTGTTTGCTGAGTCTCAAAAGCACCAGCTCATTTATCCGGTGCCAAATCTGAGGAATCTATTTCTGTTTTGCAGATCAGTGACAAGCACGATGTGGTGTTCCTCATAACAAAATATGGCTACATCCACTTGTATGACCTGGAAACTGGCACCTGTATCTACATGAACAGGATCAGTGGAGAGACCATTTTTGTTACTGCACAGCACGAAGCAACAGCTGGAATTATTGGAGTCAACAGAAAGGGACAAGTAAGGAAACTTGGCCTGGGAGCCACTTCTTTATCTAATCCCACTGGCTCTTCATGATACACTGCAGGGCTCATATCTATGTCTCAAATTTTCCAGGAATGTTCACTTTGAACTCTGCCCACAACGTGTGAGGTCTGACAGTGTTGTGAGCCACAAAATAAATTTGCTGTTCTATCTCCATACACATCTAACTTAGCTACTTTAAGCAAGTTACTAATA CHCexon5PhgAGUAFTO058 AATACCTTAATTAAACTGTTAATTGCCTGCTTTGATGCAGGCAGTGGATGACATTGGCTCTTTCTAACCAGAGGTCTCTTTAATAACATGACAAGTAGGAGGGATGAAAAACTTCCTGTGAATACCATAACTTTCCTCTTAGAAAGGCTCACTTTGGCTGAGTTTTGATATTTGGACTAACTGGAGGTTTGCCCTGGTGGTTTATTCAGGTGCTCTCAGTGTGTGTGGAAGAGGAGAACATCATTCCCTACATCACAAACGTGCTGCAGAATCCTGACCTGGCTTTACGGATGGCTGTCCGCAACAACCTGGCGGGGGCCGAGGAGCTCTTTGCCAGGAAATTCAATGCACTCTTTGCACAAGGGAACTATTCAGAGGCAGCAAAAGTGGCAGCTAATGCCCCAAAGGTAAAGTGTTCAGAACAGCACTGAACTCTACTGGCTTCAGCTTCTTGCTTCAGGAAAGCTCAGTGAATTTTTTCTCTTGTCCCAAGGTGGTACTTTGGTGCTGGGTGCTGACACTGATTGCAGGCTGGATGATATTAGAGTTTGTAAAGCCCACAGAGGAGGGGAGGAATAAATGATGAAGTAGTGGCTTTAATTCATAATATGTCTGGTACTCATCTTT ........

grep -v "#" your.vcf | cut -f 1 | uniq

ACAexon1PhgSARMA101 ACAexon2PhgMPDS1153 ARNTLexon12PhgAMANA102 BDNFexonPhgAMANA102 CALB1exon11PhgMPDS1153 CHCexon4PhgAMANA102 CHCexon5PhgAGUAFTO058 CHCexon6PhgUFAC1083 CLKexon21PhgGAPTO264 CLOCKexon6PhgGAPTO264 CLOCKexon7PhgAGUAFTO058 ......

lindenb commented 7 years ago

sorry, my bad, I wanted

cut -f 1 your.ref.fa.fai

and "cat ref.dict" please

lindenb commented 7 years ago

and the output of

grep $'ACAexon1PhgSARMA101\t117' -A1 -B1 your.vcf | cut -f 1,2,4,5

please

tcosta-f commented 7 years ago

Sure, here they are:

cut -f 1 ..../SNPs/longest_uces_semZ.fasta.fai' ACAexon1PhgSARMA101 ACAexon2PhgMPDS1153 ARNTLexon12PhgAMANA102 ARNTLexon13PhgGUR235 BDNFexonPhgAMANA102 CALB1exon11PhgMPDS1153 ....

cat '..../SNPs/longest_uces_semZ.fasta.dict' @HD VN:1.5 @SQ SN:ACAexon1PhgSARMA101 LN:309 M5:8b754971affd278122c56079aa00686c UR:file:/media/tsn/Documentos/Tiago/UCEs_Tiago/1_FINALISSIMO_Tiago_Workstation_AMNH/Pheugopedius/SNPs/longest_uces_semZ.fasta @SQ SN:ACAexon2PhgMPDS1153 LN:460 M5:9f7656caae35268bb6c018e71edbb91f UR:file:/media/tsn/Documentos/Tiago/UCEs_Tiago/1_FINALISSIMO_Tiago_Workstation_AMNH/Pheugopedius/SNPs/longest_uces_semZ.fasta @SQ SN:ARNTLexon12PhgAMANA102 LN:540 M5:527f7a783ce8e36416ba03cf01770c4a UR:file:/media/tsn/Documentos/Tiago/UCEs_Tiago/1_FINALISSIMO_Tiago_Workstation_AMNH/Pheugopedius/SNPs/longest_uces_semZ.fasta @SQ SN:ARNTLexon13PhgGUR235 LN:242 M5:2518cf757f3af9fd6f16d39e9c152ab8 UR:file:/media/tsn/Documentos/Tiago/UCEs_Tiago/1_FINALISSIMO_Tiago_Workstation_AMNH/Pheugopedius/SNPs/longest_uces_semZ.fasta @SQ SN:BDNFexonPhgAMANA102 LN:878 M5:87c57b7fefd1cc4404b67a71208fa4bb UR:file:/media/tsn/Documentos/Tiago/UCEs_Tiago/1_FINALISSIMO_Tiago_Workstation_AMNH/Pheugopedius/SNPs/longest_uces_semZ.fasta .....

grep $'ACAexon1PhgSARMA101\t117' -A1 -B1 '.../No_OUT/1SNPlocus_Pheugopedius-only-PASS-Q30-SNPs_maf0.014925373.vcf' | cut -f 1,2,4,5

CHROM POS REF ALT

ACAexon1PhgSARMA101 117 C T ACAexon2PhgMPDS1153 79 A C

lindenb commented 7 years ago

hum.. I'm puzzled for this one. Can you send the vcf and the ref fasta please ?

tcosta-f commented 7 years ago

I already uploaded them in the first comment!

What is the code that you posted?

lindenb commented 7 years ago

I already uploaded them in the first comment!

opssss, I'll check

lindenb commented 7 years ago

Sorry, I didn't see your attachement; :-(

my bug is that I 'm expecting a variant for each REF sequence. It's fixed now. Thanks for pointing this bug.

$ java -jar dist/vcf2bam.jar -R /home/lindenb/tmp/longest_uces_semZ.fa ~/tmp/1SNPlocus_Pheugopedius-only-PASS-Q30-SNPs_maf0.014925373.vcf 

@HD VN:1.5  SO:unsorted
(...)
0000000001  67  BDNFexonPhgAMANA102 1   60  100=    =   501 500 TGGTTTTAACAGTTCCACCAAGTGAGAAGAGTGATGACCATCCTTTTCTTTACTATGGTTATCTCATACTTCACTTGCATGAAAGCTGCCCCGATGAAAG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c95505  NM:i:0
0000000001  147 BDNFexonPhgAMANA102 501 60  100=    =   1   -500    GGACATGTCTGGGGCAACTGTCACAGTCCTGGAGAAAGTTCCAGTACCCAAAGGCCAACTGAAGCAATACTTCTATGAGACCAAATGCAACCCTAAGGGG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c95505  NM:i:0
0000000002  67  BDNFexonPhgAMANA102 1   60  100=    =   501 500 TGGTTTTAACAGTTCCACCAAGTGAGAAGAGTGATGACCATCCTTTTCTTTACTATGGTTATCTCATACTTCACTTGCATGAAAGCTGCCCCGATGAAAG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c95505  NM:i:0
0000000002  147 BDNFexonPhgAMANA102 501 60  100=    =   1   -500    GGACATGTCTGGGGCAACTGTCACAGTCCTGGAGAAAGTTCCAGTACCCAAAGGCCAACTGAAGCAATACTTCTATGAGACCAAATGCAACCCTAAGGGG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c95505  NM:i:0
0000000003  131 BDNFexonPhgAMANA102 1   60  100=    =   501 500 TGGTTTTAACAGTTCCACCAAGTGAGAAGAGTGATGACCATCCTTTTCTTTACTATGGTTATCTCATACTTCACTTGCATGAAAGCTGCCCCGATGAAAG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c97221  NM:i:0
0000000003  83  BDNFexonPhgAMANA102 501 60  100=    =   1   -500    GGACATGTCTGGGGCAACTGTCACAGTCCTGGAGAAAGTTCCAGTACCCAAAGGCCAACTGAAGCAATACTTCTATGAGACCAAATGCAACCCTAAGGGG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c97221  NM:i:0
0000000004  131 BDNFexonPhgAMANA102 1   60  100=    =   501 500 TGGTTTTAACAGTTCCACCAAGTGAGAAGAGTGATGACCATCCTTTTCTTTACTATGGTTATCTCATACTTCACTTGCATGAAAGCTGCCCCGATGAAAG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c97221  NM:i:0
0000000004  83  BDNFexonPhgAMANA102 501 60  100=    =   1   -500    GGACATGTCTGGGGCAACTGTCACAGTCCTGGAGAAAGTTCCAGTACCCAAAGGCCAACTGAAGCAATACTTCTATGAGACCAAATGCAACCCTAAGGGG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:Ph_c97221  NM:i:0
tcosta-f commented 7 years ago

Perfect Pierre, thank you very much!

Best,

TSN