Entering edit mode
8 weeks ago
Mahdi&Christ
▴
20
Hi, In the header of a VCF file from a disease case with several specific symptoms, some chromosome names are not typical. We plan to filter the file in later steps using a disease panel. I have three questions:
Why are these chromosome names different from the usual chromosome names?
What should we do with these unusually named chromosomes?
Should they be removed or used in the analysis steps?
I have not encountered such a case before. I would appreciate your guidance.
((((((Should I replace the file's dictionary or just filter those chromosomes?))))))
Here is my VCF file header:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=HET,Number=1,Type=Integer,Description="Position called as heterozygous (25% <= novel allele frequency <= 75%)">
##INFO=<ID=HOM,Number=1,Type=Integer,Description="Position called as homozygous: homozygous for reference (novel allele frequency < 25%) or homozygous variant (novel allele frequency > 75%)">
##INFO=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr11_gl000202_random,length=40103>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17_ctg5_hap1,length=1680828>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr17_gl000203_random,length=37498>
##contig=<ID=chr17_gl000204_random,length=81310>
##contig=<ID=chr17_gl000205_random,length=174588>
##contig=<ID=chr17_gl000206_random,length=41001>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr18_gl000207_random,length=4262>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr19_gl000208_random,length=92689>
##contig=<ID=chr19_gl000209_random,length=159169>
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr21_gl000210_random,length=27682>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4_ctg9_hap1,length=590426>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6_apd_hap1,length=4622290>
##contig=<ID=chr6_cox_hap2,length=4795371>
##contig=<ID=chr6_dbb_hap3,length=4610396>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr6_mann_hap4,length=4683263>
##contig=<ID=chr6_mcf_hap5,length=4833398>
##contig=<ID=chr6_qbl_hap6,length=4611984>
##contig=<ID=chr6_ssto_hap7,length=4928567>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr7_gl000195_random,length=182896>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr8_gl000196_random,length=38914>
##contig=<ID=chr8_gl000197_random,length=37175>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr9_gl000198_random,length=90085>
##contig=<ID=chr9_gl000199_random,length=169874>
##contig=<ID=chr9_gl000200_random,length=187035>
##contig=<ID=chr9_gl000201_random,length=36148>
##contig=<ID=chrM,length=16571>
##contig=<ID=chrUn_gl000211,length=166566>
##contig=<ID=chrUn_gl000212,length=186858>
##contig=<ID=chrUn_gl000213,length=164239>
##contig=<ID=chrUn_gl000214,length=137718>
##contig=<ID=chrUn_gl000215,length=172545>
##contig=<ID=chrUn_gl000216,length=172294>
##contig=<ID=chrUn_gl000217,length=172149>
##contig=<ID=chrUn_gl000218,length=161147>
##contig=<ID=chrUn_gl000219,length=179198>
##contig=<ID=chrUn_gl000220,length=161802>
##contig=<ID=chrUn_gl000221,length=155397>
##contig=<ID=chrUn_gl000222,length=186861>
##contig=<ID=chrUn_gl000223,length=180455>
##contig=<ID=chrUn_gl000224,length=179693>
##contig=<ID=chrUn_gl000225,length=211173>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chrUn_gl000227,length=128374>
##contig=<ID=chrUn_gl000228,length=129120>
##contig=<ID=chrUn_gl000229,length=19913>
##contig=<ID=chrUn_gl000230,length=43691>
##contig=<ID=chrUn_gl000231,length=27386>
##contig=<ID=chrUn_gl000232,length=40652>
##contig=<ID=chrUn_gl000233,length=45941>
##contig=<ID=chrUn_gl000234,length=40531>
##contig=<ID=chrUn_gl000235,length=34474>
##contig=<ID=chrUn_gl000236,length=41934>
##contig=<ID=chrUn_gl000237,length=45867>
##contig=<ID=chrUn_gl000238,length=39939>
##contig=<ID=chrUn_gl000239,length=33824>
##contig=<ID=chrUn_gl000240,length=41933>
##contig=<ID=chrUn_gl000241,length=42152>
##contig=<ID=chrUn_gl000242,length=43523>
##contig=<ID=chrUn_gl000243,length=43341>
##contig=<ID=chrUn_gl000244,length=39929>
##contig=<ID=chrUn_gl000245,length=36651>
##contig=<ID=chrUn_gl000246,length=38154>
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chrUn_gl000249,length=38502>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
And these are those chromosome names I mentioned:
chr11_gl000202_random
chr17_ctg5_hap1
chr17_gl000203_random
chr17_gl000204_random
chr17_gl000205_random
chr17_gl000206_random
chr18_gl000207_random
chr19_gl000208_random
chr19_gl000209_random
chr1_gl000191_random
chr1_gl000192_random
chr21_gl000210_random
chr4_ctg9_hap1
chr4_gl000193_random
chr4_gl000194_random
chr6_apd_hap1
chr6_cox_hap2
chr6_dbb_hap3
chr6_mann_hap4
chr6_mcf_hap5
chr6_qbl_hap6
chr6_ssto_hap7
chr7_gl000195_random
chr8_gl000196_random
chr8_gl000197_random
chr9_gl000198_random
chr9_gl000199_random
chr9_gl000200_random
chr9_gl000201_random
chrUn_gl000211
chrUn_gl000212
chrUn_gl000213
chrUn_gl000214
chrUn_gl000215
chrUn_gl000216
chrUn_gl000217
chrUn_gl000218
chrUn_gl000219
chrUn_gl000220
chrUn_gl000221
chrUn_gl000222
chrUn_gl000223
chrUn_gl000224
chrUn_gl000225
chrUn_gl000226
chrUn_gl000227
chrUn_gl000228
chrUn_gl000229
chrUn_gl000230
chrUn_gl000231
chrUn_gl000232
chrUn_gl000233
chrUn_gl000234
chrUn_gl000235
chrUn_gl000236
chrUn_gl000237
chrUn_gl000238
chrUn_gl000239
chrUn_gl000240
chrUn_gl000241
chrUn_gl000242
chrUn_gl000243
chrUn_gl000244
chrUn_gl000245
chrUn_gl000246
chrUn_gl000247
chrUn_gl000248
chrUn_gl000249
