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pairix

This modification can do double-chromosome indexing/query as an option. The text file must be first sorted by two chromosome columns and then by the first position column. The file must be compressed using bgzip. The index has an extension .px2.

installation

git clone https://github.com/SooLepairix.git
cd pairix
make
# add the bin path to PATH

Usage

# compression
bgzip textfile

# indexing
pairix -s<chr1_column> [-d<chr2_column>] -b<pos1_start_column> -e<pos1_end_column> [-u<pos2_start_column> -v<pos2_end_column>] textfile.gz    # u, v is required for full 2d query.

# querying
pairix textfile.gz region1 [region2 [...]]  ## region is in the following format.
pairix textfile.gz '<chr1>:<start1>-<end1>[|<chr2>:<start2>-<end2>]'    # make sure to quote, so '|' is not interpreted as a pipe.

Note

  • Currently 2D indexing supports only 2D query and 1D indexing supports only 1D query. Ideally, it will be extended to support 1D query for 2D indexed files. (future plan)
  • The index produced by this modified pairix is not compatible with the original pairix index. They are based on different structures.
  • Note that if the chromosome pair block are ordered in a way that the first coordinate is always smaller than the second ('upper-triangle'), a lower-triangle query will return an empty result. For example, if there is a block with chr1='6' and chr2='X', but not with chr1='X' and chr2='6', then the query for X|6 will not return any result. The search is not symmetric.

Example

Preparing a double-chromosome-block sorted text file

(column 2 and 6 are chromosomes (chr1 and chr2), column 3 is position of the first coordinate (pos1)).

# the following has already be done and the final merged_nodup.tab.chrblock_sorted.txt.gz is already in the samples folder.
cut -d' ' -f1-8 /n/data1/hms/dbmi/park/sl325/juicer/SRR1658832/aligned.20160803/merged_nodups.txt | sort -t' ' -k2,2 -k6,6 -k3,3g - > merged_nodup.chrblock_sorted.txt
sed 's/ /\t/g' merged_nodup.chrblock_sorted.txt > samples/merged_nodup.tab.chrblock_sorted.txt   ## note that sed may not work for every implementation.
head samples/merged_nodup.tab.chrblock_sorted.txt

0	1	49819	93	0	1	16858344	44945
0	1	108364	242	16	1	255090	508
16	1	108871	246	16	1	222643221	508360
0	1	110012	248	16	1	116929	264
0	1	114876	256	0	1	156133	357
0	1	122900	271	0	1	224115759	511974
0	1	128053	280	0	1	129622	284
16	1	128155	280	16	1	251467	498
0	1	139312	305	0	1	141553	315
0	1	142396	316	0	1	222981299	509189

bgzipping

bgzip samples/merged_nodup.tab.chrblock_sorted.txt

2D indexing & query on the above file

2D indexing with pairix on chromosome pair (-s2 -d6) and the position of the first chromosome (b3). For full 2D query, also add -u7 and -v7, the start and end positions of the second coordinate. They are not used for indexing per se, but the column index is stored as part of the index, which allows full 2D query through individual comparisons.

pairix -f -s2 -d6 -b3 -e3 -u7 samples/merged_nodup.tab.chrblock_sorted.txt.gz

semi 2D query (chr10:1-1000000 x chr20)

pairix samples/merged_nodup.tab.chrblock_sorted.txt.gz '10:1-1000000|20'
0	10	624779	1361	0	20	40941397	97868
16	10	948577	2120	16	20	59816485	148396

full 2D query (chr10:1-1000000 x chr20:50000000-60000000)

pairix samples/merged_nodup.tab.chrblock_sorted.txt.gz '10:1-1000000|20:50000000-60000000'
16	10	948577	2120	16	20	59816485	148396

full 2D multi-query (chr1:1-10000000 x chr20:50000000-60000000 AND 3:5000000-9000000 x X:70000000-90000000)

pairix samples/merged_nodup.tab.chrblock_sorted.txt.gz '1:1-10000000|20:50000000-60000000' '3:5000000-9000000|X:70000000-90000000'
16	1	4717358	10139	16	20	55598650	138321
0	1	5649238	12370	16	20	59660150	148059
16	1	6651242	15069	0	20	50444303	124692
0	1	6930805	15906	16	20	50655496	125483
0	1	8555535	20339	0	20	55253919	137318
16	3	5025392	11911	16	X	86766531	207787
0	3	5298790	12678	0	X	84731179	203102
0	3	7272964	17297	0	X	88560374	211726
16	3	8402388	19935	16	X	77717595	187377

1D indexing on a regular vcf file, bgzipped.

1D indexing

pairix -s1 -b2 -e2 -f samples/SRR1171591.variants.snp.vqsr.p.vcf.gz

1D query

pairix samples/SRR1171591.variants.snp.vqsr.p.vcf.gz chr10:1-4000000
chr10	3463966	.	C	T	51.74	PASS	AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;VQSLOD=7.88;culprit=FS	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
chr10	3978708	rs29320259	T	C	1916.77	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.016;DB;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=629.1968;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;MQRankSum=0.773;POSITIVE_TRAIN_SITE;QD=28.61;ReadPosRankSum=0.500;VQSLOD=3.29;culprit=FS	GT:AD:DP:GQ:PL	1/1:3,64:67:70:1945,70,0
chr10	3978709	.	G	A	1901.77	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.677;DB;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=579.9049;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;MQRankSum=0.308;POSITIVE_TRAIN_SITE;QD=28.81;ReadPosRankSum=0.585;VQSLOD=3.24;culprit=FS	GT:AD:DP:GQ:PL	1/1:3,63:66:73:1930,73,0