BamPhased01

Extract Reads from a SAM/BAM file supporting at least two variants in a VCF file.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bamphased01  [options] Files

Usage: bamphased01 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --buffer-size
      When we're looking for variants in a lare VCF file, load the variants in 
      an interval of 'N' bases instead of doing a random access for each 
      variant. 
      Default: 1000
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ignore-discordant-rg
      In paired mode, ignore discordant read-groups RG-ID.
      Default: false
    --mapq0
      If set. Do not remove the reads failing the test but set the MAPQ to 0.
      Default: false
    --min-supporting
      Min number of variants that should be supported by one read.
      Default: 2
    -o, --out
      Output file. Optional . Default: stdout
    --paired
      Activate Paired-end mode. Variant can be supported by the read or/and is 
      mate. Input must be sorted on query name using for example 'samtools 
      collate'. 
      Default: false
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --regions
      Limit analysis to this interval. A source of intervals. The following 
      suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, 
      gtf.gz.Otherwise it could be an empty string (no interval) or a list of 
      plain interval separated by '[ \t\n;,]'
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --tag
      Tag in metadata of read containing the variants positions. Ignored if 
      empty 
      Default: XP
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
  * -V, --vcf
      Indexed VCf file
    --version
      print version and exit

Keywords

• vcf
• phased
• genotypes
• bam

Creation Date

20210218

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/phased/BamPhased01.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite bamphased01 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

for @isamtalves

Only diallelic SNV are supported.

Example

$ java -jar dist/bamphased01.jar \
    -V src/test/resources/rotavirus_rf.vcf.gz \
    src/test/resources/S4.bam 


@HD VN:1.6  SO:coordinate
@SQ SN:RF01 LN:3302
@SQ SN:RF02 LN:2687
@SQ SN:RF03 LN:2592
@SQ SN:RF04 LN:2362
@SQ SN:RF05 LN:1579
@SQ SN:RF06 LN:1356
@SQ SN:RF07 LN:1074
@SQ SN:RF08 LN:1059
@SQ SN:RF09 LN:1062
@SQ SN:RF10 LN:751
@SQ SN:RF11 LN:666
@RG ID:S4   SM:S4   LB:L4   CN:Nantes
@PG ID:0    CL:-V src/test/resources/rotavirus_rf.vcf.gz src/test/resources/S4.bam  VN:04c54fe  PN:bamphased01
@CO bamphased01. compilation:20210218183501 githash:04c54fe htsjdk:2.23.0 date:20210218183539. cmd:-V src/test/resources/rotavirus_rf.vcf.gz src/test/resources/S4.bam
RF10_109_650_2:2:0_2:0:0_13 99  RF10    109 60  70M =   581 542 CGATACTCGAGGATCCAGGGATGGCGTATTATCCTTATCTAGCAACTGTCCTAACAGTTTTGTTCAGGTT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S4 NM:i:4  XP:Z:RF10_139_T_A;RF10_175_C_G  AS:i:51 XS:i:0
RF10_128_592_1:2:0_1:0:0_27 163 RF10    128 60  70M =   523 465 GATGGCGTATTATCCTTAAATAGCATCTGTCCTAACAGTTTTGTTCAGGTTGCACAAAGCATCTATTCCA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S4 NM:i:3  XP:Z:RF10_139_T_A;RF10_175_C_G  AS:i:55 XS:i:0
RF10_133_733_1:2:0_1:0:0_f  99  RF10    133 60  70M =   664 601 CGTATTATCCTTATATAGCAACTGTCCTAACAGTTTTGTTCAGGTTGCACAAAGCATCTATTCCAACAAT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S4 NM:i:3  XP:Z:RF10_139_T_A;RF10_175_C_G  AS:i:55 XS:i:0
RF10_137_727_1:2:0_2:0:0_8  163 RF10    137 60  70M =   658 591 TTATCCTTATATAGCATCTGTCCTAACAGTTTTGTTCAGGTTGCACAAAGCATCTATTGCAACAATGAAA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S4 NM:i:3  XP:Z:RF10_139_T_A;RF10_175_C_G  AS:i:57 XS:i:0
RF10_138_562_1:2:0_1:0:0_1e 163 RF10    138 60  70M =   493 425 TATCCTTATATAGCATCTGTCCTAACAGTTATGTTCAGGTTGCACAAAGCATCTATTCCAACAATGAAAA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S4 NM:i:3  XP:Z:RF10_139_T_A;RF10_175_C_G  AS:i:58 XS:i:0

paired mode:

$ samtools sort -n -T xx src/test/resources/S2.bam | \
    java -jar dist/bamphased01.jar -V src/test/resources/rotavirus_rf.vcf.gz   --min-supporting 2 --paired --ignore-discordant-rg

@HD VN:1.6  SO:queryname
@SQ SN:RF01 LN:3302
@SQ SN:RF02 LN:2687
@SQ SN:RF03 LN:2592
@SQ SN:RF04 LN:2362
@SQ SN:RF05 LN:1579
@SQ SN:RF06 LN:1356
@SQ SN:RF07 LN:1074
@SQ SN:RF08 LN:1059
@SQ SN:RF09 LN:1062
@SQ SN:RF10 LN:751
@SQ SN:RF11 LN:666
@RG ID:S2   SM:S2   LB:L2   CN:Nantes
@PG ID:0    PN:bamphased01  VN:5d263eb  CL:-V src/test/resources/rotavirus_rf.vcf.gz --min-supporting 2 --paired --ignore-discordant-rg
@CO bamphased01. compilation:20210220193801 githash:5d263eb htsjdk:2.23.0 date:20210220193911. cmd:-V src/test/resources/rotavirus_rf.vcf.gz --min-supporting 2 --paired --ignore-discordant-rg
RF03_2142_2592_1:1:0_2:1:0_1c   99  RF03    2142    60  70M =   2523    451 AACTATTTTATTGGAATTAAGTTCAAAAATATACCCTATGAATATGATGATAAAGTACCCCATCTTACAT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:2  XP:Z:RF03_2201_G_C;RF03_2573_A_G    AS:i:60 XS:i:0
RF03_2142_2592_1:1:0_2:1:0_1c   147 RF03    2523    60  70M =   2142    -451    ATAAAAGGCGACACACTGTTAGATATGACTGAGTGAGCTAAAAACTTAACGCACTGGTCACATCGTGACC  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:3  XP:Z:RF03_2201_G_C;RF03_2573_A_G    AS:i:55 XS:i:0
RF05_813_1307_2:1:0_1:1:0_10    99  RF05    813 60  70M =   1238    495 AAAGCGTGAACGCATATAGTTGATGCTAGAAATTATATTAGTATTATGAACTCATCGTATACTGAGAATT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:3  XP:Z:RF05_879_C_A;RF05_1297_T_G AS:i:56 XS:i:0
RF05_813_1307_2:1:0_1:1:0_10    147 RF05    1238    60  70M =   813 -495    CATAAATGGAACGGAGTATGTATTATTAGACTATGAAGTGAACTGGGAAGTGAGGGGACGAGTCAGGCAA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:2  XP:Z:RF05_879_C_A;RF05_1297_T_G AS:i:60 XS:i:0
RF05_829_1327_3:1:0_4:1:0_16    99  RF05    829 60  70M =   1258    499 TCGTTGATGCTCGAAATTATATTAGTATTATGAAGTCATCGTATACTGAGAATTACAGTGTGTCACAAAG  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:4  XP:Z:RF05_879_C_A;RF05_1297_T_G AS:i:53 XS:i:0
RF05_829_1327_3:1:0_4:1:0_16    147 RF05    1258    60  70M =   829 -499    TATTATTAGACTATCAAGTGAACTGGGAAGTGAGGGGACGAGTCATGCATAACAGGGATGCGAAAGTACC  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:5  XP:Z:RF05_879_C_A;RF05_1297_T_G AS:i:45 XS:i:0
RF05_843_1306_0:1:0_2:1:0_23    83  RF05    1237    60  70M =   843 -464    ACATAAATCGAACCGAGTATGTATTATTAGACTATGAAGTGAACTGGGAAGTGAGGGGACGAGTCATGCA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:3  XP:Z:RF05_1297_T_G;RF05_879_C_A AS:i:55 XS:i:0
RF05_843_1306_0:1:0_2:1:0_23    163 RF05    843 60  70M =   1237    464 AATTATATTAGTATTATGAACTCATCGTATACTGAGAATTACAGTGTGTCACAAAGATGTAAATTGTTTA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:1  XP:Z:RF05_1297_T_G;RF05_879_C_A AS:i:65 XS:i:0
RF05_857_1394_2:1:0_1:1:0_2f    99  RF05    857 60  70M =   1325    538 TATGAACTCATCGTATACTGAGAATTACAGTGTGTCACAAAGATGTACATTGATTACTAAGTATAAATTT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:3  XP:Z:RF05_879_C_A;RF05_1339_A_C AS:i:55 XS:i:0
RF05_857_1394_2:1:0_1:1:0_2f    147 RF05    1325    60  70M =   857 -538    TCCAAGAATTTTGACTATGAATGATACAAAGAAGATACTGAGTGCAATGATATTTGACTGGTTTGACACA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:2  XP:Z:RF05_879_C_A;RF05_1339_A_C AS:i:64 XS:i:0
RF05_863_1322_3:1:0_0:1:0_0 83  RF05    1253    60  70M =   863 -460    GTATGTATTATTAGACTATGAAGTGAACTGGGAAGTGAGGGGACGAGTCATGCAAAACATGGATGGGAAA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:1  XP:Z:RF05_1297_T_G;RF05_879_C_A AS:i:65 XS:i:0
RF05_863_1322_3:1:0_0:1:0_0 163 RF05    863 60  70M =   1253    460 CTCATCGTATACTGAGAATTACAGTTTGTCACAAAGATGTAAAATGTTTACTAAGTATAAATATGGGATT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:4  XP:Z:RF05_1297_T_G;RF05_879_C_A AS:i:50 XS:i:0
RF05_874_1375_3:1:0_1:1:0_4d    99  RF05    874 60  70M =   1306    502 CTGAGAATTACAGTGTGTCACAAAGATTTAAATTGTTTACTAAGTATACATTTGGGATTGTATCAAGATA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:4  XP:Z:RF05_879_C_A;RF05_1339_A_C AS:i:54 XS:i:0
RF05_874_1375_3:1:0_1:1:0_4d    147 RF05    1306    60  70M =   874 -502    AAAACATGGATGGGAAAGTACCAAGAATTTTGACTATGAATGATACAAAGAAGATACTCAGTGCAATGAT  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:2  XP:Z:RF05_879_C_A;RF05_1339_A_C AS:i:60 XS:i:0
RF05_916_1354_3:0:0_1:2:0_53    147 RF05    1285    60  70M =   916 -439    AAGTGAGGGGAAGAGTCATGCAAAACATGGATGGGAAAGTACCAAGAATTTTGACTATGAATGATACAAA  2222222222222222222222222222222222222222222222222222222222222222222222  PG:Z:0  RG:Z:S2 NM:i:3  XP:Z:RF05_1297_T_G;RF05_1339_A_C    AS:i:55 XS:i:0

See also

• Biostar9501110