Generate VCF File from Bam file and fasta by GATK

Question

[misbahabas]

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

[WouterDeCoster]

You should show the command you used and the full error you got, this is not the entire message.

[TriS]

check whether the chromosome names are the same in the reference and the bam file. i.e.

grep ">" myRef.fa

and

samtools view myBam.bam | head

after you do that, try the ALLOW_SEQ_DICT_INCOMPATIBILITY option

[misbahabas]

thanks for reply but I successfully generated vcf file by GATK using follow ing command

java -jar GenomeAnalysisTK.jar -R /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/misbah_test_folder/DQ1_annotation/ucsc_canfam3/canFam3.fa -T UnifiedGenotyper -maxAltAlleles 15 -I /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/dog_bamfiles/dq1_bam_test/chr1.bam -o /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/misbah_test_folder/DQ1_annotation/ucsc_canfam3/unified_output.raw.snps.indels.g.vcf

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

[WouterDeCoster]

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?

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[misbahabas]

Thanks its helpful