I found out that there were more data not used by Sara in her alignment:

Hi, Xiaojiang & Adam,

Per Xiaojiang’s presentation, it seems that we had three lanes of DNAseq. I used alignment Sara provided when I did ASE analysis. I would give it a try at least on the parental strains to see any changes with the SNV calls.  Your any attention will be appreciated.

FYI, the following were the files I used:

##===================================================================================
#ID     NISC_raw_BAM    NTP_ID  genotype
sample1 111025_MORPHEUS_D09D9ACXX.4.bam NTP_02_DNA      BL6 male
sample2 110922_MORPHEUS_C052AACXX.1.bam NTP_15_DNA      BL6 female
sample3 110922_MORPHEUS_C052AACXX.2.bam NTP_25_DNA      C3H male
sample4 110922_MORPHEUS_C052AACXX.4.bam NTP_32_DNA      C3H female
sample5 110922_MORPHEUS_C052AACXX.8.bam NTP_213_DNA     F1 male from NTP-02/32 [BL6m x C3Hf]
sample6 110922_MORPHEUS_C052AACXX.7.bam NTP_221_DNA     F1 female from NTP-02/32 [BL6m x C3Hf]
sample7 111014_NIOBE_C0522ACXX.8.bam    NTP-121_DNA     F1 male from NTP-15/25 [BL6f x C3Hm]
sample8 110922_MORPHEUS_C052AACXX.5.bam NTP_123_DNA     F1 female from NTP-15/25 [BL6f x C3Hm]
##===================================================================================

Thanks.

Jianying Li

Adam provided information on all the available data

Hi Jianying,

The DNA-seq raw data can be found in /ddn/gs1/project/mousemeth/DNAseq/raw_reads/NISC_111018.  There are 3 lanes each for NTP_15_DNA (BL6 female) and NTP_32_DNA (C3H female), and 1 each for the rest.  The BAM files contained in this directory were aligned with ELAND by the NISC pipeline, so you will probably want to start with the FASTQs.

Thanks,

Adam

So, I have to re-align all the data and call SNP myself.

Step 1. Create a new folder: SNPcalling under ~/project2013/
Step 2. Align raw files into mm9
[li11@ehscmplp14/bioinfo2 NISC_111018]$ ls -l NTP_15_*
-r--r--r-- 1 burkholderab ngsuser 56026816392 Oct 18  2011 NTP_15_DNA_110922_MORPHEUS_C052AACXX.1.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 56026816392 Oct 18  2011 NTP_15_DNA_110922_MORPHEUS_C052AACXX.1.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 41436725311 Oct 18  2011 NTP_15_DNA_110922_MORPHEUS_C052AACXX.1.bam
-r--r--r-- 1 burkholderab ngsuser 52997281364 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.5.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 52997281364 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.5.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 38105590148 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.5.bam
-r--r--r-- 1 burkholderab ngsuser 52256364140 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.6.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 52256364140 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.6.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 37258274997 Dec  5  2011 NTP_15_DNA_111115_NIOBE_D0B7PACXX.6.bam
[li11@ehscmplp14/bioinfo2 NISC_111018]$ ls -l NTP_32_*
-r--r--r-- 1 burkholderab ngsuser 42257747650 Oct 18  2011 NTP_32_DNA_110922_MORPHEUS_C052AACXX.4.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 42257747650 Oct 18  2011 NTP_32_DNA_110922_MORPHEUS_C052AACXX.4.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 28324903863 Oct 18  2011 NTP_32_DNA_110922_MORPHEUS_C052AACXX.4.bam
-r--r--r-- 1 burkholderab ngsuser 42775914395 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.7.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 42775914395 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.7.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 29834785339 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.7.bam
-r--r--r-- 1 burkholderab ngsuser 42938647452 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.8.1.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 42938647452 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.8.2.sanger.fastq
-r--r--r-- 1 burkholderab ngsuser 30675427143 Dec  5  2011 NTP_32_DNA_111115_NIOBE_D0B7PACXX.8.bam