Generate VCF File from Bam file and fasta by GATK
Aslamu ALikum
I want to make vcf file from bam file usin GATK tool but it give error when run the command
03025958, chrUn_AAEX03025959, chrUn_AAEX03025960, chrUn_AAEX03025961, chrUn_AAEX03025962, chrUn_AAEX03025963, chrUn_AAEX03025964, chrUn_AAEX03025965, chrUn_AAEX03025966, chrUn_AAEX03025967, chrUn_AAEX03025968, chrUn_AAEX03025969, chrUn_AAEX03025970, chrUn_AAEX03025971, chrUn_AAEX03025972, chrUn_AAEX03025973, chrUn_AAEX03025974, chrUn_AAEX03025975, chrUn_AAEX03025976, chrUn_AAEX03025977, chrUn_AAEX03025978, chrUn_AAEX03025979, chrUn_AAEX03025980, chrUn_AAEX03025981, chrUn_AAEX03025982, chrUn_AAEX03025983, chrUn_AAEX03025984, chrUn_AAEX03025985, chrUn_AAEX03025986, chrUn_AAEX03025987, chrUn_AAEX03025988, chrUn_AAEX03025989, chrUn_AAEX03025990, chrUn_AAEX03025991, chrUn_AAEX03025992, chrUn_AAEX03025993, chrUn_AAEX03025994, chrUn_AAEX03025995, chrUn_AAEX03025996, chrUn_AAEX03025997, chrUn_AAEX03025998, chrUn_AAEX03025999, chrUn_AAEX03026000, chrUn_AAEX03026001, chrUn_AAEX03026002, chrUn_AAEX03026003, chrUn_AAEX03026004, chrUn_AAEX03026005, chrUn_AAEX03026006, chrUn_AAEX03026007, chrUn_AAEX03026008, chrUn_AAEX03026009, chrUn_AAEX03026010, chrUn_AAEX03026011, chrUn_AAEX03026012, chrUn_AAEX03026013, chrUn_AAEX03026014, chrUn_AAEX03026015, chrUn_AAEX03026016, chrUn_AAEX03026017, chrUn_AAEX03026018, chrUn_AAEX03026019, chrUn_AAEX03026020, chrUn_AAEX03026021, chrUn_AAEX03026022, chrUn_AAEX03026023, chrUn_AAEX03026024, chrUn_AAEX03026025, chrUn_AAEX03026026, chrUn_AAEX03026027, chrUn_AAEX03026028, chrUn_AAEX03026029, chrUn_AAEX03026030, chrUn_AAEX03026031, chrUn_AAEX03026032, chrUn_AAEX03026033, chrUn_AAEX03026034, chrUn_AAEX03026035, chrUn_AAEX03026036, chrUn_AAEX03026037, chrUn_AAEX03026038, chrUn_AAEX03026039, chrUn_AAEX03026040, chrUn_AAEX03026041, chrUn_AAEX03026042, chrUn_AAEX03026043, chrUn_AAEX03026044, chrUn_AAEX03026045, chrUn_AAEX03026046, chrUn_AAEX03026047, chrUn_AAEX03026048, chrUn_AAEX03026049, chrUn_AAEX03026050, chrUn_AAEX03026051, chrUn_AAEX03026052, chrUn_AAEX03026053, chrUn_AAEX03026054, chrUn_AAEX03026055, chrUn_AAEX03026056, chrUn_AAEX03026057, chrUn_AAEX03026058, chrUn_AAEX03026059, chrUn_AAEX03026060, chrUn_AAEX03026061, chrUn_AAEX03026062, chrUn_AAEX03026063, chrUn_AAEX03026064, chrUn_AAEX03026065, chrUn_AAEX03026066, chrUn_AAEX03026067, chrUn_AAEX03026068, chrUn_AAEX03026069, chrUn_AAEX03026070, chrUn_AAEX03026071, chrUn_AAEX03026072, chrM
##### ERROR reference contigs = 1
I used bam file and fasta sequence to generate vcf
Please tell me about this error,
Thanks in advance
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misbahabas •
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You should show the command you used and the full error you got, this is not the entire message.
check whether the chromosome names are the same in the reference and the bam file. i.e.
and
after you do that, try the
ALLOW_SEQ_DICT_INCOMPATIBILITYoptionthanks for reply but I successfully generated vcf file by GATK using follow ing command
I used this vcf file for further annotation by snpeff. but now i am confused between haplotypecaller and UnifiedGenotyper. which is best one. Kindly tell me which one is good for this purpose
A simple google search for "haplotypecaller unifiedgenotyper" brings up the following thread on the GATK forum: Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?
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Thanks its helpful